Dear Lane and SEEKR2 team, After successful installation, I'm tried running the examples given on this github page, but I'm getting the subject error in the run.py step (details below). This problem seems to be similar to one reported on the openmm issue page, but not being an expert I thought it's better to take your advice before trying to upgrade anything in CUDA installation. This cuda version is working well with Amber18. Can you please have a look and let me know how to try and fix this problem and proceed further? Looking forward to hearing from you and the team. thank you and best regards. Dr Vaibhav A. Dixit, Asst. Prof., BITS Pilani, Pilani, India.

relevant openmm issue page

https://github.com/openmm/openmm/issues/2251

(SEEKR) [exx@c107739 seekr2]$ which nvcc /usr/local/cuda/bin/nvcc (SEEKR) [exx@c107739 seekr2]$ nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2019 NVIDIA Corporation Built on Sun_Jul_28_19:07:16_PDT_2019 Cuda compilation tools, release 10.1, V10.1.243 (SEEKR) [exx@c107739 seekr2]$

(SEEKR) [exx@c107739 seekr2]$ python3.8 run.py any ~/test_mmvt_openmm/model.xml anchor 0 has not run the minimum number of steps 0 of 100000 anchor 1 has not run the minimum number of steps 0 of 100000 anchor 2 has not run the minimum number of steps 0 of 100000 anchor 3 has not run the minimum number of steps 0 of 100000 anchor 4 has not run the minimum number of steps 0 of 100000 anchor 5 has not run the minimum number of steps 0 of 100000 anchor 6 has not run the minimum number of steps 0 of 100000 anchor 7 has not run the minimum number of steps 0 of 100000 anchor 8 has not run the minimum number of steps 0 of 100000 anchor 9 has not run the minimum number of steps 0 of 100000 anchor 10 has not run the minimum number of steps 0 of 100000 anchor 11 has not run the minimum number of steps 0 of 100000 anchor 12 has not run the minimum number of steps 0 of 100000 running anchor_index: 0 restart: False total_simulation_length: 100000 num_transitions: 0 Traceback (most recent call last): File "run.py", line 742, in run(model, instruction, min_total_simulation_length, File "run.py", line 515, in run run_openmm(model, anchor_index, restart, File "run.py", line 404, in run_openmm sim_openmm_obj = mmvt_sim_openmm.create_sim_openmm( File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 168, in create_sim_openmm add_simulation(sim_openmm, model, topology, positions, box_vectors) File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 101, in add_simulation sim_openmm.simulation = openmm_app.Simulation( File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 105, in init self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 13232, in init _openmm.Context_swiginit(self, _openmm.new_Context(*args)) simtk.openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_INVALID_PTX (218) (SEEKR) [exx@c107739 seekr2]$

Dear Vaibhav, I think it would be useful to know how you have installed seekr2? Especially, if you used conda or compiled from source.

I believe, the seekr2-openmm-plugin which is accessible by conda-forge comes precompiled against cuda10.2. Perhaps this is already the issue but Lane is the expert here.

Best regards Jens Wilbert

Dear Jens, OK, I think I'm able to understand the incompatibility that you've described. I created a SEEKR environment in conda, then installed python3.8, then used conda to install the seekr2-openmm-plugin and seekr2. (FYI - Lane is already aware of my installation failure/success attempts, thus I'll also wait for him to suggest further things to try). thanks and best regards. Vaibhav

Hi Vaibhav, Greeting from the SEEKR team. One of the possible sources of error may be the fact that OpenMM is using CPU as the default platform. Can you make sure you have installed OpenMM from source instead of conda. If no, please do that. If you need further help, do let me know.

On Wed, Sep 1, 2021 at 8:02 AM bensebaer @.***> wrote:

Dear Vaibhav, I think it would be useful to know how you have installed seekr2? Especially, if you used conda or compiled from source.

I believe, the seekr2-openmm-plugin which is accessible by conda-forge comes precompiled against cuda10.2. Perhaps this is already the issue but Lane is the expert here.

Best regards Jens Wilbert

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A. Anand Ojha Graduate Student Researcher,

Department of Chemistry and Biochemistry, University of California San Diego

Hi Anand, thanks for your response. I have earlier interacted with Lane, who recommended creating a SEEKR environment in python3.8 and then calling openmm modules. Below is the usage that is currently showing that it is installed as per suggestions. Please let me know additional info about the current installation is required. thanks (base) [exx@c107739 ~]$ conda activate SEEKR (SEEKR) [exx@c107739 ~]$ python3.8 Python 3.8.10 | packaged by conda-forge | (default, May 11 2021, 07:01:05) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

from simtk import openmm

Hii Vaibhav, Can you please check the output of the following command :

python -m simtk.testInstallation

On Wed, Sep 1, 2021 at 8:12 AM vaibhavadixit @.***> wrote:

Dear Jens, OK, I think I'm able to understand the incompatibility that you've described. I created a SEEKR environment conda, then installed python3.8, then used conda to install the seekr2-openmm-plugin and seekr2. (FYI - Lane is already aware of my installation failure/success attempts, thus I'll also wait for him to suggest further things to try). thanks and best regards. Vaibhav

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/seekrcentral/seekr2/issues/8#issuecomment-910224527, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEFQUROQ35MMSNKINGHFGTT7YKB3ANCNFSM5DGFTJ4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- With Regards,

A. Anand Ojha Graduate Student Researcher,

Department of Chemistry and Biochemistry, University of California San Diego

Hi Anand, Your suspicion was correct, I'm getting the following which shows that cuda gives error. Please do let me know what you think would be the best options to try now. thanks.

(base) [exx@c107739 ~]$ conda activate SEEKR (SEEKR) [exx@c107739 ~]$ python -m simtk.testInstallation

OpenMM Version: 7.5.1 Git Revision: a9cfd7fb9343e21c3dbb76e377c721328830a3ee

There are 4 Platforms available:

1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 CUDA - Error computing forces with CUDA platform 4 OpenCL - Successfully computed forces

CUDA platform error: Error loading CUDA module: CUDA_ERROR_INVALID_PTX (218)

Median difference in forces between platforms:

Reference vs. CPU: 6.29101e-06 Reference vs. OpenCL: 6.75475e-06 CPU vs. OpenCL: 8.07327e-07

All differences are within tolerance. (SEEKR) [exx@c107739 ~]$

Hello,

Thanks @anandojha and @bensebaer for your comments and assistance.

Yes, as the linked OpenMM issue suggested, this error is caused by a driver incompatibility or also an incompatible GPU. Do you know what type of GPU you are using and whether it is compatible with CUDA 10.2? (The command "nvidia-smi" might work, and it will tell you your driver versions, CUDA version, and what GPUs you have).

I noticed from your first post that the nvcc version you are using is for CUDA 10.1, which is not compatible with the latest OpenMM and, by extension, SEEKR2. How did you install that version? Was that CUDA build from your previous attempts at installation? One solution would be to uninstall your CUDA 10.1, then retry the SEEKR2 installation, and Conda should at least pull the correct version of CudaTools. Or you could try to install CUDA 10.2 manually. The best choice depends on your situation.

Dear Lane, I have RTX2080 GPU hardware as shown below. Is it possible to install cuda 10.2 in the seekr environment without affecting the older version on which my current Amber18 installation depends? If this is possible then I will do that and try to reinstall seekr2. Please let me know. thanks

+-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | 1 2363 G /usr/bin/X 148MiB | | 1 3233 G /usr/bin/gnome-shell 124MiB | | 1 56760 G ...AAAAAAAAAAAACAAAAAAAAAA= --shared-files 83MiB | +-----------------------------------------------------------------------------+ (base) [user@localhost ~]$

OK thanks for that information. Yes, your RTX2080s should work just fine, and the driver version looks recent enough. Your Nvidia-smi command shows that it thinks you have Cuda10.2. Do you have multiple Cuda installations? You should look in /usr/local/ to see.

There may be some possible options for you:

You could try to install (or find, if it's already installed) CUDA 10.2 (or later) in addition to CUDA10.1, and then set the OPENMM_CUDA_COMPILER environmental variable to point to the CUDA 10.2 nvcc path, but somehow point Amber18 to the 10.1 version (probably another environmental variable).
You might be able to install an older version of OpenMM that was compatible with Cuda10.1 and then install SEEKR2 on top of that (probably not a good idea, and you'd probably need to install the seekr2 openmm plugin from source on top of it).
You might be able to make the SEEKR conda environment ignore the installed CUDA by setting the CUDA_HOME and CUDA_ROOT environmental variables to empty for the environment (other variables might need to be set to empty as well), then when you install the seekr2 openmm plugin, it should install the proper version of CudaToolkit.

Hi, I tried the first option suggested by Lane and installed cuda 10.2 as suggested here and nvcc --version returns cuda 10.2. But I'm still getting driver errors. Can you please check and suggest to me what to try next?

https://www.server-world.info/en/note?os=CentOS_7&p=cuda&f=4

(SEEKR) [exx@c107739 seekr2]$ nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2019 NVIDIA Corporation Built on Wed_Oct_23_19:24:38_PDT_2019 Cuda compilation tools, release 10.2, V10.2.89 (SEEKR) [exx@c107739 seekr2]$

(SEEKR) [exx@c107739 seekr2]$ python3.8 run.py any ~/test_mmvt_openmm/model.xml anchor 0 has not run the minimum number of steps 0 of 100000 anchor 1 has not run the minimum number of steps 0 of 100000 anchor 2 has not run the minimum number of steps 0 of 100000 anchor 3 has not run the minimum number of steps 0 of 100000 anchor 4 has not run the minimum number of steps 0 of 100000 anchor 5 has not run the minimum number of steps 0 of 100000 anchor 6 has not run the minimum number of steps 0 of 100000 anchor 7 has not run the minimum number of steps 0 of 100000 anchor 8 has not run the minimum number of steps 0 of 100000 anchor 9 has not run the minimum number of steps 0 of 100000 anchor 10 has not run the minimum number of steps 0 of 100000 anchor 11 has not run the minimum number of steps 0 of 100000 anchor 12 has not run the minimum number of steps 0 of 100000 running anchor_index: 0 restart: False total_simulation_length: 100000 num_transitions: 0 Traceback (most recent call last): File "run.py", line 742, in run(model, instruction, min_total_simulation_length, File "run.py", line 515, in run run_openmm(model, anchor_index, restart, File "run.py", line 404, in run_openmm sim_openmm_obj = mmvt_sim_openmm.create_sim_openmm( File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 168, in create_sim_openmm add_simulation(sim_openmm, model, topology, positions, box_vectors) File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 101, in add_simulation sim_openmm.simulation = openmm_app.Simulation( File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 105, in init self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 13232, in init _openmm.Context_swiginit(self, _openmm.new_Context(*args)) simtk.openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_SYSTEM_DRIVER_MISMATCH (803) at /home/conda/feedstock_root/build_artifacts/openmm_1622798691062/work/platforms/cuda/src/CudaContext.cpp:138 (SEEKR) [exx@c107739 seekr2]$

Hi SEEKR team, To my surprise, the calculations seem to be running just fine (after there was a reboot due to power failure) and I accidentally decided to run the tests/tutorial case anyway. Can you please have a look and let me know if it is doing things as expected? Can you please suggest a set of commands that can print the full setup on which SEEKR2 is depending here? This will help me try to reproduce the installation on another GPU similar system that I have in the lab. I wasn't expecting a reboot to fix something for me here (which can often happen in windows OS). Did I just got lucky here due to some OS update in the background or I did something to fix it without realizing it myself? Looking forward to your confirmation and suggestions. thank you and best regards.

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69144.49079205882,297.4233782909998,52.56848950689602 20000,-69869.93366379052,301.560597952733,52.56848950689602 30000,-69864.64904012525,296.51825589367263,52.56848950689602 40000,-69377.52449393808,302.80793589861304,52.56848950689602 50000,-69721.83292784536,292.03861392671246,52.56848950689602 60000,-70285.15553236526,298.7569602733776,52.56848950689602 70000,-69477.06213368417,302.12781557852315,52.56848950689602 80000,-69412.19511798577,298.04278694035133,52.56848950689602 90000,-69802.81410196872,302.73667807143323,52.56848950689602 100000,-69872.02696706454,300.25169928173386,52.56848950689602 Benchmark (ns/day): 676.0865219728388 running anchor_index: 1 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69701.0679280666,299.9465145748033,53.001182076839996 20000,-68875.80444348347,291.08401098832985,53.001182076839996 30000,-69407.27905209706,295.04682130819543,53.001182076839996 40000,-69374.98674597323,296.5943957999594,53.001182076839996 50000,-69510.50046643266,297.4515442928506,53.001182076839996 60000,-69487.54161233205,300.2598541155219,53.001182076839996 70000,-69621.41305995733,300.3923321056398,53.001182076839996 80000,-69524.28550882259,303.74551240996215,53.001182076839996 90000,-70045.26211276255,311.0443026811395,53.001182076839996 100000,-69362.11746455648,296.17904476577297,53.001182076839996 Benchmark (ns/day): 661.0541200182117 running anchor_index: 2 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69785.76114975323,296.46893362002567,53.001182076839996 20000,-69200.05805598001,296.41330462774545,53.001182076839996 30000,-69295.07416729943,302.4301459305852,53.001182076839996 40000,-69281.83241042274,301.9972234557154,53.001182076839996 50000,-69091.48401152418,295.9802550223431,53.001182076839996 60000,-69381.06063582585,294.0204234760598,53.001182076839996 70000,-69486.26055974478,298.1119611029692,53.001182076839996 80000,-69115.26048954594,299.44512274838866,53.001182076839996 90000,-69300.33501393104,296.359589787676,53.001182076839996 100000,-69486.955681903,307.9725501983454,53.001182076839996 Benchmark (ns/day): 656.2592886141096 running anchor_index: 3 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69737.18051548884,294.5279735085756,53.001182076839996 20000,-69392.46493441012,293.44891176706403,53.001182076839996 30000,-69498.79043459706,303.006132158916,53.001182076839996 40000,-69175.29168446176,294.6025852434763,53.001182076839996 50000,-69383.68013051013,306.0325861102716,53.001182076839996 60000,-69961.78327824437,294.75652817405745,53.001182076839996 70000,-69871.04464263469,299.42534139155663,53.001182076839996 80000,-69456.92276385019,300.3888699871004,53.001182076839996 90000,-69786.59675886354,298.23651743435175,53.001182076839996 100000,-69643.17584280891,298.11451407893713,53.001182076839996 Benchmark (ns/day): 614.2356845813468 running anchor_index: 4 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69386.6953338632,303.95054076402243,53.001182076839996 20000,-69253.00790108804,300.47427564619716,53.001182076839996 30000,-69465.83993170381,292.36135086040895,53.001182076839996 40000,-69448.45238402707,295.603624863649,53.001182076839996 50000,-69452.6658732178,305.1601520774961,53.001182076839996 60000,-69162.39610835159,300.0348418201349,53.001182076839996 70000,-69205.13485659898,291.70067787432737,53.001182076839996 80000,-69333.56733806909,293.75808921470457,53.001182076839996 90000,-69219.3913178423,298.9393149480047,53.001182076839996 100000,-69191.19156954251,295.99066890970664,53.001182076839996 Benchmark (ns/day): 617.8916371039779 running anchor_index: 5 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69457.26372874231,298.5604264331683,53.001182076839996 20000,-69605.07306833827,304.36473799555705,53.001182076839996 30000,-69276.33479454223,299.89061760295914,53.001182076839996 40000,-69371.19127700396,298.2033213307406,53.001182076839996 50000,-69446.38602255401,299.05456112032755,53.001182076839996 60000,-68944.29696569016,291.75485399398684,53.001182076839996 70000,-69678.53721238917,299.12353092231524,53.001182076839996 80000,-69207.1422912617,293.6369841531982,53.001182076839996 90000,-69158.74460100941,294.2481936769401,53.001182076839996 100000,-69736.93902522675,300.350724483127,53.001182076839996 Benchmark (ns/day): 635.8922623463477 running anchor_index: 6 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69251.31409991405,300.405627763369,53.001182076839996 20000,-69504.57336028386,303.30762338068723,53.001182076839996 30000,-69881.59594982542,297.0480543670246,53.001182076839996 40000,-69196.91975443647,296.54985897734304,53.001182076839996 50000,-69337.93296267267,302.9833374553011,53.001182076839996 60000,-69786.15843727044,298.66235433774364,53.001182076839996 70000,-69565.88825172913,310.51878997243443,53.001182076839996 80000,-69561.05699932424,296.2620756755379,53.001182076839996 90000,-68921.38426727621,293.9531165881675,53.001182076839996 100000,-69359.30978567398,298.37334101205585,53.001182076839996 Benchmark (ns/day): 640.9204718489292 running anchor_index: 7 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69362.65660170786,298.4715200397846,53.001182076839996 20000,-69459.3173377564,294.9194907853032,53.001182076839996 30000,-69137.4052030241,305.3206715784008,53.001182076839996 40000,-69733.47936457687,298.550087659625,53.001182076839996 50000,-69206.60384401074,304.203192377914,53.001182076839996 60000,-69728.44668358349,302.77903815229723,53.001182076839996 70000,-69640.23172272567,296.61623855379094,53.001182076839996 80000,-69180.34710867377,298.3687018439519,53.001182076839996 90000,-69913.56008797663,296.9220362845659,53.001182076839996 100000,-69325.02275857137,290.20203682225156,53.001182076839996 Benchmark (ns/day): 621.8316666762902 running anchor_index: 8 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-68739.53935059876,289.42954985552257,53.001182076839996 20000,-69121.00007149944,299.9123223974211,53.001182076839996 30000,-69811.68617732049,296.477888605543,53.001182076839996 40000,-69093.4523969164,295.3691913464193,53.001182076839996 50000,-69373.34382889944,299.4915681131448,53.001182076839996 60000,-69568.40951526398,308.6268661829777,53.001182076839996 70000,-69318.72763755795,295.679862981259,53.001182076839996 80000,-69550.27482223621,294.32184033944105,53.001182076839996 90000,-69380.45023123675,296.3258739871022,53.001182076839996 100000,-69723.430675623,289.9096700042352,53.001182076839996 Benchmark (ns/day): 648.3124859183208 running anchor_index: 9 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69858.92770797084,291.9108298301936,53.001182076839996 20000,-69792.74257540028,296.94819340770266,53.001182076839996 30000,-69147.37162053975,306.5790999340041,53.001182076839996 40000,-69840.14387600496,298.09405670187914,53.001182076839996 50000,-69124.67333274201,290.6085592263482,53.001182076839996 60000,-69837.37839602039,292.0942978063598,53.001182076839996 70000,-69220.87221926934,292.0224410766485,53.001182076839996 80000,-69529.60648475884,303.9038645638152,53.001182076839996 90000,-69695.44364100188,303.63866094972843,53.001182076839996 100000,-69796.55966087629,305.4785144705075,53.001182076839996 Benchmark (ns/day): 618.3341983021858 running anchor_index: 10 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-68734.58490729053,290.97723757808507,53.001182076839996 20000,-69255.29286105372,299.26811022468314,53.001182076839996 30000,-69180.11697052879,302.9003978966918,53.001182076839996 40000,-69909.11901671207,306.9346781786293,53.001182076839996 50000,-69607.68029917893,303.12062335102496,53.001182076839996 60000,-69131.29972944304,300.0868214441313,53.001182076839996 70000,-69479.25102394383,296.8862636112948,53.001182076839996 80000,-69484.68777931464,298.91813823296667,53.001182076839996 90000,-69448.93743409216,296.58130712262135,53.001182076839996 100000,-69244.11212478636,299.0142822728575,53.001182076839996 Benchmark (ns/day): 620.5240910663637 running anchor_index: 11 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69604.82230700646,291.95329672997866,53.001182076839996 20000,-69510.67855428415,295.80811020616716,53.001182076839996 30000,-69396.76138013112,299.307601813386,53.001182076839996 40000,-70003.28882299172,303.74270547547115,53.001182076839996 50000,-69500.36680087273,303.5304438083032,53.001182076839996 60000,-69442.89330834162,291.56155136654564,53.001182076839996 70000,-69363.14966853557,301.3103345014555,53.001182076839996 80000,-69963.57409431,298.82918600416957,53.001182076839996 90000,-69208.87962260656,301.6396460181288,53.001182076839996 100000,-69553.3454008653,298.0939068570571,53.001182076839996 Benchmark (ns/day): 621.1309564011887 running anchor_index: 12 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69175.02726903511,296.3507783306151,53.001182076839996 20000,-69305.08690150117,300.6441185317881,53.001182076839996 30000,-69498.77728664369,301.5865100771034,53.001182076839996 40000,-69378.32120181562,296.7177506805017,53.001182076839996 50000,-69597.09609594557,296.0285238252822,53.001182076839996 60000,-69285.1623312519,298.64573238303086,53.001182076839996 70000,-69805.5251628966,294.6759730709682,53.001182076839996 80000,-69298.1716454933,300.49698663034195,53.001182076839996 90000,-69851.00703219848,299.06179501114514,53.001182076839996 100000,-69256.60992451839,298.7163790259338,53.001182076839996 Benchmark (ns/day): 643.8215685422085 running BD: b_surface restart: False trajectories to run: 10000 transitions so far: 0 moving to directory: /home/exx/test_mmvt_openmm/b_surface running command: bd_top input.xml command surface_spheres -probe_radius 1.5 < hostguest_receptor.xml > receptor_surface.xml command inside_points -spheres hostguest_receptor.xml -surface receptor_surface.xml -egrid receptor2.dx > receptor_inside.xml command hydro_params < receptor_inside.xml > receptor_hydro_params.xml command test_charges < hostguest_receptor.xml > receptor_charges.xml command lumped_charges -pts receptor_charges.xml > receptor_cheby.xml command make_surface_sphere_list -surface receptor_surface.xml -spheres hostguest_receptor.xml -rxn rxns.xml -group receptor -core receptor > receptor_surface_atoms.xml command mpole_grid_fit -dx receptor0.dx -solvdi 78 -debye 1.79769e+308 > receptor_mpole.xml command born_integral -in receptor_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > receptor_born.dx command compute_charges_squared < receptor_charges.xml > receptor_charges_squared.xml command lumped_charges -pts receptor_charges_squared.xml > receptor_squared_cheby.xml command surface_spheres -probe_radius 1.5 < hostguest_ligand.xml > ligand_surface.xml command inside_points -spheres hostguest_ligand.xml -surface ligand_surface.xml -egrid ligand2.dx > ligand_inside.xml command hydro_params < ligand_inside.xml > ligand_hydro_params.xml command test_charges < hostguest_ligand.xml > ligand_charges.xml command lumped_charges -pts ligand_charges.xml > ligand_cheby.xml command make_surface_sphere_list -surface ligand_surface.xml -spheres hostguest_ligand.xml -rxn rxns.xml -group ligand -core ligand > ligand_surface_atoms.xml command mpole_grid_fit -dx ligand0.dx -solvdi 78 -debye 1.79769e+308 > ligand_mpole.xml command born_integral -in ligand_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > ligand_born.dx command compute_charges_squared < ligand_charges.xml > ligand_charges_squared.xml command lumped_charges -pts ligand_charges_squared.xml > ligand_squared_cheby.xml moving to directory: /home/exx/test_mmvt_openmm/b_surface running command: nam_simulation receptor_ligand_simulation.xml BrownDye 2.0: Version of 21 Jul 2021

Hi Vaibhav, yes it seems to run fine. There are two things you can check.

Is the OpenMM using Cuda or CPU
Sometimes, when we reboot, and the system updates, a few Cuda crashed library files get updated, so might have solved the issue. But, in almost the majority of the cases, CUDA is the major issue and it depends majorly from system to system.

On Fri, Sep 3, 2021 at 11:22 PM vaibhavadixit @.***> wrote:

Hi SEEKR team, To my surprise, the calculations seem to be running just fine (after there was a reboot due to power failure) and I accidentally decided to run the tests/tutorial case anyway. Can you please have a look and let me know if it is doing things as expected? Can you please suggest a set of commands that can print the full setup on which SEEKR2 is depending here? This will help me try to reproduce the installation on another GPU similar system that I have in the lab. I wasn't expecting a reboot to fix something for me here (which can often happen in windows OS). Did I just got lucky here due to some OS update in the background or I did something to fix it without realizing it myself? Looking forward to your confirmation and suggestions. thank you and best regards.

(SEEKR) @.*** seekr2]$ python3.8 run.py any ~/test_mmvt_openmm/model.xml anchor 0 has not run the minimum number of steps 0 of 100000 anchor 1 has not run the minimum number of steps 0 of 100000 anchor 2 has not run the minimum number of steps 0 of 100000 anchor 3 has not run the minimum number of steps 0 of 100000 anchor 4 has not run the minimum number of steps 0 of 100000 anchor 5 has not run the minimum number of steps 0 of 100000 anchor 6 has not run the minimum number of steps 0 of 100000 anchor 7 has not run the minimum number of steps 0 of 100000 anchor 8 has not run the minimum number of steps 0 of 100000 anchor 9 has not run the minimum number of steps 0 of 100000 anchor 10 has not run the minimum number of steps 0 of 100000 anchor 11 has not run the minimum number of steps 0 of 100000 anchor 12 has not run the minimum number of steps 0 of 100000 running anchor_index: 0 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69144.49079205882,297.4233782909998,52.56848950689602 20000,-69869.93366379052,301.560597952733,52.56848950689602 30000,-69864.64904012525,296.51825589367263,52.56848950689602 40000,-69377.52449393808,302.80793589861304,52.56848950689602 50000,-69721.83292784536,292.03861392671246,52.56848950689602 60000,-70285.15553236526,298.7569602733776,52.56848950689602 70000,-69477.06213368417,302.12781557852315,52.56848950689602 80000,-69412.19511798577,298.04278694035133,52.56848950689602 90000,-69802.81410196872,302.73667807143323,52.56848950689602 100000,-69872.02696706454,300.25169928173386,52.56848950689602 Benchmark (ns/day): 676.0865219728388 running anchor_index: 1 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69701.0679280666,299.9465145748033,53.001182076839996 20000,-68875.80444348347,291.08401098832985,53.001182076839996 30000,-69407.27905209706,295.04682130819543,53.001182076839996 40000,-69374.98674597323,296.5943957999594,53.001182076839996 50000,-69510.50046643266,297.4515442928506,53.001182076839996 60000,-69487.54161233205,300.2598541155219,53.001182076839996 70000,-69621.41305995733,300.3923321056398,53.001182076839996 80000,-69524.28550882259,303.74551240996215,53.001182076839996 90000,-70045.26211276255,311.0443026811395,53.001182076839996 100000,-69362.11746455648,296.17904476577297,53.001182076839996 Benchmark (ns/day): 661.0541200182117 running anchor_index: 2 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69785.76114975323,296.46893362002567,53.001182076839996 20000,-69200.05805598001,296.41330462774545,53.001182076839996 30000,-69295.07416729943,302.4301459305852,53.001182076839996 40000,-69281.83241042274,301.9972234557154,53.001182076839996 50000,-69091.48401152418,295.9802550223431,53.001182076839996 60000,-69381.06063582585,294.0204234760598,53.001182076839996 70000,-69486.26055974478,298.1119611029692,53.001182076839996 80000,-69115.26048954594,299.44512274838866,53.001182076839996 90000,-69300.33501393104,296.359589787676,53.001182076839996 100000,-69486.955681903,307.9725501983454,53.001182076839996 Benchmark (ns/day): 656.2592886141096 running anchor_index: 3 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69737.18051548884,294.5279735085756,53.001182076839996 20000,-69392.46493441012,293.44891176706403,53.001182076839996 30000,-69498.79043459706,303.006132158916,53.001182076839996 40000,-69175.29168446176,294.6025852434763,53.001182076839996 50000,-69383.68013051013,306.0325861102716,53.001182076839996 60000,-69961.78327824437,294.75652817405745,53.001182076839996 70000,-69871.04464263469,299.42534139155663,53.001182076839996 80000,-69456.92276385019,300.3888699871004,53.001182076839996 90000,-69786.59675886354,298.23651743435175,53.001182076839996 100000,-69643.17584280891,298.11451407893713,53.001182076839996 Benchmark (ns/day): 614.2356845813468 running anchor_index: 4 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69386.6953338632,303.95054076402243,53.001182076839996 20000,-69253.00790108804,300.47427564619716,53.001182076839996 30000,-69465.83993170381,292.36135086040895,53.001182076839996 40000,-69448.45238402707,295.603624863649,53.001182076839996 50000,-69452.6658732178,305.1601520774961,53.001182076839996 60000,-69162.39610835159,300.0348418201349,53.001182076839996 70000,-69205.13485659898,291.70067787432737,53.001182076839996 80000,-69333.56733806909,293.75808921470457,53.001182076839996 90000,-69219.3913178423,298.9393149480047,53.001182076839996 100000,-69191.19156954251,295.99066890970664,53.001182076839996 Benchmark (ns/day): 617.8916371039779 running anchor_index: 5 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69457.26372874231,298.5604264331683,53.001182076839996 20000,-69605.07306833827,304.36473799555705,53.001182076839996 30000,-69276.33479454223,299.89061760295914,53.001182076839996 40000,-69371.19127700396,298.2033213307406,53.001182076839996 50000,-69446.38602255401,299.05456112032755,53.001182076839996 60000,-68944.29696569016,291.75485399398684,53.001182076839996 70000,-69678.53721238917,299.12353092231524,53.001182076839996 80000,-69207.1422912617,293.6369841531982,53.001182076839996 90000,-69158.74460100941,294.2481936769401,53.001182076839996 100000,-69736.93902522675,300.350724483127,53.001182076839996 Benchmark (ns/day): 635.8922623463477 running anchor_index: 6 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69251.31409991405,300.405627763369,53.001182076839996 20000,-69504.57336028386,303.30762338068723,53.001182076839996 30000,-69881.59594982542,297.0480543670246,53.001182076839996 40000,-69196.91975443647,296.54985897734304,53.001182076839996 50000,-69337.93296267267,302.9833374553011,53.001182076839996 60000,-69786.15843727044,298.66235433774364,53.001182076839996 70000,-69565.88825172913,310.51878997243443,53.001182076839996 80000,-69561.05699932424,296.2620756755379,53.001182076839996 90000,-68921.38426727621,293.9531165881675,53.001182076839996 100000,-69359.30978567398,298.37334101205585,53.001182076839996 Benchmark (ns/day): 640.9204718489292 running anchor_index: 7 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69362.65660170786,298.4715200397846,53.001182076839996 20000,-69459.3173377564,294.9194907853032,53.001182076839996 30000,-69137.4052030241,305.3206715784008,53.001182076839996 40000,-69733.47936457687,298.550087659625,53.001182076839996 50000,-69206.60384401074,304.203192377914,53.001182076839996 60000,-69728.44668358349,302.77903815229723,53.001182076839996 70000,-69640.23172272567,296.61623855379094,53.001182076839996 80000,-69180.34710867377,298.3687018439519,53.001182076839996 90000,-69913.56008797663,296.9220362845659,53.001182076839996 100000,-69325.02275857137,290.20203682225156,53.001182076839996 Benchmark (ns/day): 621.8316666762902 running anchor_index: 8 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-68739.53935059876,289.42954985552257,53.001182076839996 20000,-69121.00007149944,299.9123223974211,53.001182076839996 30000,-69811.68617732049,296.477888605543,53.001182076839996 40000,-69093.4523969164,295.3691913464193,53.001182076839996 50000,-69373.34382889944,299.4915681131448,53.001182076839996 60000,-69568.40951526398,308.6268661829777,53.001182076839996 70000,-69318.72763755795,295.679862981259,53.001182076839996 80000,-69550.27482223621,294.32184033944105,53.001182076839996 90000,-69380.45023123675,296.3258739871022,53.001182076839996 100000,-69723.430675623,289.9096700042352,53.001182076839996 Benchmark (ns/day): 648.3124859183208 running anchor_index: 9 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69858.92770797084,291.9108298301936,53.001182076839996 20000,-69792.74257540028,296.94819340770266,53.001182076839996 30000,-69147.37162053975,306.5790999340041,53.001182076839996 40000,-69840.14387600496,298.09405670187914,53.001182076839996 50000,-69124.67333274201,290.6085592263482,53.001182076839996 60000,-69837.37839602039,292.0942978063598,53.001182076839996 70000,-69220.87221926934,292.0224410766485,53.001182076839996 80000,-69529.60648475884,303.9038645638152,53.001182076839996 90000,-69695.44364100188,303.63866094972843,53.001182076839996 100000,-69796.55966087629,305.4785144705075,53.001182076839996 Benchmark (ns/day): 618.3341983021858 running anchor_index: 10 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-68734.58490729053,290.97723757808507,53.001182076839996 20000,-69255.29286105372,299.26811022468314,53.001182076839996 30000,-69180.11697052879,302.9003978966918,53.001182076839996 40000,-69909.11901671207,306.9346781786293,53.001182076839996 50000,-69607.68029917893,303.12062335102496,53.001182076839996 60000,-69131.29972944304,300.0868214441313,53.001182076839996 70000,-69479.25102394383,296.8862636112948,53.001182076839996 80000,-69484.68777931464,298.91813823296667,53.001182076839996 90000,-69448.93743409216,296.58130712262135,53.001182076839996 100000,-69244.11212478636,299.0142822728575,53.001182076839996 Benchmark (ns/day): 620.5240910663637 running anchor_index: 11 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69604.82230700646,291.95329672997866,53.001182076839996 20000,-69510.67855428415,295.80811020616716,53.001182076839996 30000,-69396.76138013112,299.307601813386,53.001182076839996 40000,-70003.28882299172,303.74270547547115,53.001182076839996 50000,-69500.36680087273,303.5304438083032,53.001182076839996 60000,-69442.89330834162,291.56155136654564,53.001182076839996 70000,-69363.14966853557,301.3103345014555,53.001182076839996 80000,-69963.57409431,298.82918600416957,53.001182076839996 90000,-69208.87962260656,301.6396460181288,53.001182076839996 100000,-69553.3454008653,298.0939068570571,53.001182076839996 Benchmark (ns/day): 621.1309564011887 running anchor_index: 12 restart: False total_simulation_length: 100000 num_transitions: 0

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

10000,-69175.02726903511,296.3507783306151,53.001182076839996 20000,-69305.08690150117,300.6441185317881,53.001182076839996 30000,-69498.77728664369,301.5865100771034,53.001182076839996 40000,-69378.32120181562,296.7177506805017,53.001182076839996 50000,-69597.09609594557,296.0285238252822,53.001182076839996 60000,-69285.1623312519,298.64573238303086,53.001182076839996 70000,-69805.5251628966,294.6759730709682,53.001182076839996 80000,-69298.1716454933,300.49698663034195,53.001182076839996 90000,-69851.00703219848,299.06179501114514,53.001182076839996 100000,-69256.60992451839,298.7163790259338,53.001182076839996 Benchmark (ns/day): 643.8215685422085 running BD: b_surface restart: False trajectories to run: 10000 transitions so far: 0 moving to directory: /home/exx/test_mmvt_openmm/b_surface running command: bd_top input.xml command surface_spheres -probe_radius 1.5 < hostguest_receptor.xml > receptor_surface.xml command inside_points -spheres hostguest_receptor.xml -surface receptor_surface.xml -egrid receptor2.dx > receptor_inside.xml command hydro_params < receptor_inside.xml > receptor_hydro_params.xml command test_charges < hostguest_receptor.xml > receptor_charges.xml command lumped_charges -pts receptor_charges.xml > receptor_cheby.xml command make_surface_sphere_list -surface receptor_surface.xml -spheres hostguest_receptor.xml -rxn rxns.xml -group receptor -core receptor > receptor_surface_atoms.xml command mpole_grid_fit -dx receptor0.dx -solvdi 78 -debye 1.79769e+308 > receptor_mpole.xml command born_integral -in receptor_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > receptor_born.dx command compute_charges_squared < receptor_charges.xml > receptor_charges_squared.xml command lumped_charges -pts receptor_charges_squared.xml > receptor_squared_cheby.xml command surface_spheres -probe_radius 1.5 < hostguest_ligand.xml > ligand_surface.xml command inside_points -spheres hostguest_ligand.xml -surface ligand_surface.xml -egrid ligand2.dx > ligand_inside.xml command hydro_params < ligand_inside.xml > ligand_hydro_params.xml command test_charges < hostguest_ligand.xml > ligand_charges.xml command lumped_charges -pts ligand_charges.xml > ligand_cheby.xml command make_surface_sphere_list -surface ligand_surface.xml -spheres hostguest_ligand.xml -rxn rxns.xml -group ligand -core ligand > ligand_surface_atoms.xml command mpole_grid_fit -dx ligand0.dx -solvdi 78 -debye 1.79769e+308 > ligand_mpole.xml command born_integral -in ligand_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > ligand_born.dx command compute_charges_squared < ligand_charges.xml > ligand_charges_squared.xml command lumped_charges -pts ligand_charges_squared.xml > ligand_squared_cheby.xml moving to directory: /home/exx/test_mmvt_openmm/b_surface running command: nam_simulation receptor_ligand_simulation.xml BrownDye 2.0: Version of 21 Jul 2021

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-- With Regards,

A. Anand Ojha Graduate Student Researcher,

Department of Chemistry and Biochemistry, University of California San Diego

Hi All and @anandojha, This is somewhat disappointing because it means that it would take more than standard effort to install it on a new system each time. Do you have a sort of idea/benchmark on differences in results that might arise due to different installation details? I reran the simtk.testInstallation option, which suggests that CUDA version is working now. But which output file can I check to know/test if a calculation used the CUDA-GPU? The calculation is already over thus can't check it with the nvidia-smi option, right?

Regarding the tutorial/test case: The run step finished without errors and did not print anything additional beyond what I shared in the last message, but. The next "converge" and analyze steps ran only when I invoked python3.8. Can you please check if it converged and was analyzed correctly? It looks like it failed more than a couple of times. Thus do I need to change the input and start thinking about the science (milestoning theory) based changes in the input. Please suggest. Looking forward to your valuable suggestions and comments. thanks and best regards.

(SEEKR) [exx@c107739 seekr2]$ python3.8 -m simtk.testInstallation

OpenMM Version: 7.5.1 Git Revision: a9cfd7fb9343e21c3dbb76e377c721328830a3ee

There are 4 Platforms available:

1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 CUDA - Successfully computed forces 4 OpenCL - Successfully computed forces

Median difference in forces between platforms:

Reference vs. CPU: 6.29272e-06 Reference vs. CUDA: 6.74111e-06 CPU vs. CUDA: 7.36849e-07 Reference vs. OpenCL: 6.75475e-06 CPU vs. OpenCL: 8.03983e-07 CUDA vs. OpenCL: 2.67005e-07

All differences are within tolerance. (SEEKR) [exx@c107739 seekr2]$

(SEEKR) [exx@c107739 seekr2]$ python converge.py ~/test_mmvt_openmm/model.xml Traceback (most recent call last): File "converge.py", line 9, in import argparse ImportError: No module named argparse (SEEKR) [exx@c107739 seekr2]$ python3.8 converge.py ~/test_mmvt_openmm/model.xml All available options for --k_on_state include: [0] No BD milestone has been provided for k_on_state. The BD milestone 0 has been chosen by default. Processing interval 0 of 100 Processing interval 10 of 100 Processing interval 20 of 100 Processing interval 30 of 100 Processing interval 40 of 100 Processing interval 50 of 100 Processing interval 60 of 100 Processing interval 70 of 100 Processing interval 80 of 100 Processing interval 90 of 100 All plots have been saved to: /home/exx/test_mmvt_openmm/images_and_plots/ Molecular dynamics results:

Anchor 0: Milestone transitions: 0->0 : 165, Milestone avg. transition time (ps): (0, 0) : 1.193, Convergence value: 6.0899e-03. Converged? True
Anchor 1: Milestone transitions: 0->1 : 16, 1->0 : 16, Milestone avg. transition time (ps): 0 : 8.382, 1 : 3.977, Convergence value: 1.4208e-02. Converged? False
Anchor 2: Milestone transitions: 2->1 : 12, 1->2 : 11, Milestone avg. transition time (ps): 2 : 1.119, 1 : 15.319, Convergence value: 4.4027e-02. Converged? False
Anchor 3: Milestone transitions: 2->3 : 25, 3->2 : 24, Milestone avg. transition time (ps): 2 : 3.560, 3 : 4.354, Convergence value: 1.5193e-02. Converged? False
Anchor 4: Milestone transitions: 3->4 : 30, 4->3 : 30, Milestone avg. transition time (ps): 3 : 4.569, 4 : 1.976, Convergence value: 1.4800e-02. Converged? False
Anchor 5: Milestone transitions: 5->4 : 39, 4->5 : 39, Milestone avg. transition time (ps): 5 : 1.756, 4 : 3.271, Convergence value: 2.1740e-02. Converged? False
Anchor 6: Milestone transitions: 6->5 : 24, 5->6 : 23, Milestone avg. transition time (ps): 6 : 4.478, 5 : 3.476, Convergence value: 9.6712e-03. Converged? False
Anchor 7: Milestone transitions: 7->6 : 23, 6->7 : 22, Milestone avg. transition time (ps): 7 : 4.550, 6 : 4.079, Convergence value: 6.3605e-03. Converged? False
Anchor 8: Milestone transitions: 8->7 : 29, 7->8 : 28, Milestone avg. transition time (ps): 8 : 3.782, 7 : 2.884, Convergence value: 8.4210e-03. Converged? False
Anchor 9: Milestone transitions: 9->8 : 21, 8->9 : 21, Milestone avg. transition time (ps): 9 : 5.848, 8 : 3.112, Convergence value: 1.1400e-02. Converged? False
Anchor 10: Milestone transitions: 9->10 : 19, 10->9 : 18, Milestone avg. transition time (ps): 9 : 6.821, 10 : 3.433, Convergence value: 9.9480e-03. Converged? False
Anchor 11: Milestone transitions: 10->11 : 30, 11->10 : 30, Milestone avg. transition time (ps): 10 : 3.122, 11 : 3.429, Convergence value: 5.6892e-03. Converged? False
Anchor 12: Milestone transitions: 12->11 : 32, 11->12 : 31, Milestone avg. transition time (ps): 12 : 4.020, 11 : 2.067, Convergence value: 7.0283e-03. Converged? False Brownian dynamics results:
b-surface reaction counts: to milestone 12: 4817 to milestone 11: 2404 to escaped: 7596 to stuck: 0
BD milestone 0 reaction counts: to milestone 11: 2404 to escaped: 2413 (SEEKR) [exx@c107739 seekr2]$ python3.8 analyze.py ~/test_mmvt_openmm/model.xml All post-simulation checks passed. Printing results from MMVT SEEKR calculation k_off (1/s): (1.27 ± 0.18) 10^+07 k_ons : k_on (1/s 1/M) to state 0 : (3.570 ± 0.052) 10^+08 Dissociation constant (M) to state 0 : (3.56 ± 0.50) 10^-02 ΔG (kcal/mol) to state 0 : (-1.976 ± 0.083) 10^+00 Mean first passage times (s): MFPT from state 0 to state bulk : (7.9 ± 1.0) 10^-08 All plots being saved to: /home/exx/test_mmvt_openmm/images_and_plots/ (SEEKR) [exx@c107739 seekr2]$

This issue was resolved by restarting the computer.

seekrcentral / seekr2

simtk.openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_INVALID_PTX (218) #8

relevant openmm issue page

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"

"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"