drroe
commented
5 years ago I'll probably need files so I can reproduce the error. The topology and a few coordinate frames should suffice.
Open DDGmichigan opened 5 years ago
drroe
commented
5 years ago I'll probably need files so I can reproduce the error. The topology and a few coordinate frames should suffice.
DDGmichigan
commented
5 years ago Sure Dan. I will send them to you asap. Thanks for replying
DDGmichigan
commented
5 years ago drroe
commented
5 years ago Thanks for the files. However, I wasn't able to reproduce the segfault (using version 4.12.1). Could you send me the peaks file you are using as well? Also the input you used to generate the peaks file (in particular, I would like to see the exact volmap command you used). I'll paste the input I successfully used below.
Also, I noticed some issues with how you are currently doing your calculation. If you look at the output from the autoimage command you'll notice that your C3N residues are "fixed" to your anchor (which you probably do not want) because they are not considered solvent molecules by default. You should add the following before autoimage:
solvent :WAT,C3NMy volmap input:
parm 3kfa_layer_ACN_H2O_5-95vv.prmtop
trajin New4E_production.1.crd
solvent :C3N,WAT
autoimage
strip :Cl-,Na+
rms first mass out 3kfa_ACN_15-20ns_md_CA_rmsd.txt :1-286@CA
volmap :C3N centermask ^1 buffer 5.0 peakfile 3kfa_ACN_peak.xyz dx 1.0My spam input:
parm 3kfa_layer_ACN_H2O_5-95vv.prmtop
trajin New4E_production.1.crd
solvent :WAT,C3N
autoimage
strip :Cl-,Na+
rms first mass out 3kfa_ACN_15-20ns_md_CA_rmsd.txt :1-286@CA
spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 \
dgbulk -30.3 dhbulk -22.2 info info.txt summary spam_summary.out \
out spam_energies.outHi, Sounds weird as to why I am getting the error! Attached is a peakfile input I used. I have also attached a file MixMD_energies.pdb , it contains the x,y,z coordinates followed by net free energy of binding at that hotspot. sample file looks like this ATOM 1 XX UNX A 1 -6.000 14.000 -2.500 0.00 -1.880542 ATOM 1 XX UNX A 2 -4.500 16.000 -7.000 0.00 -1.864117 ATOM 1 XX UNX A 3 0.000 0.500 12.000 0.00 -1.668812 ATOM 1 XX UNX A 4 1.000 -3.500 9.500 0.00 -1.621935 ATOM 1 XX UNX A 5 4.000 23.000 -3.500 0.00 -1.465110 ATOM 1 XX UNX A 6 0.000 22.000 20.500 0.00 -1.435783
I have a small script which converts this file to peakfile.xyz. When this failed, I got segfault errors, I used the volmap command to generate the peakfile My vomap command is " volmap volmap_C3N.xplor 0.5 0.5 0.5 :C3N@C2 name GRID size 200,200,200 peakcut 0.001 peakfile 3kfa_ACN_peak.xyz"
Even then the error files.zip persisted
drroe
commented
5 years ago Even with your peaks file, I can't reproduce the segfault. I checked with valgrind and there are no memory shenanigans going on. Can you post the output of cpptraj --internal-version?
Can you try running with the input I provided (both for generating the peaks with volmap and the spam command) and see if you still get the segfault?
DDGmichigan
commented
5 years ago [3kfa_ACN_xplor_bind_energ_last5ns_10runs]$ cpptraj --version CPPTRAJ: Version V4.12.2 (GitHub) Its my bad luck that the error is not popping up today, maybe it was a bad day yesterday when I tried, let me try it once more and then shall get back to you. I did not mean to waste your valuable time over this. I am sorry!
drroe
commented
5 years ago No worries - code should never segfault so I'd like to get to the bottom of it. If you can still reproduce the segfault I may have you run valgrind to do a more in-depth memory check if you don't mind.
DDGmichigan
commented
5 years ago Absolutely! I am sitting with it today afternoon and shall get back to you with updates! Thanks for being so helpful Regards Debarati
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No worries - code should never segfault so I'd like to get to the bottom of it. If you can still reproduce the segfault I may have you run valgrind to do a more in-depth memory check if you don't mind.
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DDGmichigan
commented
5 years ago Hi Daniel, There is no segfault issues now with SPAM but I have some scientific queries.
When I look at hotspots and evaluate the free energies of binding of ACN molecules on those hotspots I get negative energies of binding! When I used the SPAM command to calculate the interaction energies, I get positive dG values which cannot be possible ideally, any clues as to what might be going on with the SPAM calculations. It would immensely help This is the output file named "SPAM_Summary.out"
1.000 3.8280 3.3674 0.4606 5.000 3.8842 2.6350 1.2492 7.000 4.0662 3.2994 0.7668 11.000 2.0295 3.1875 -1.1581 14.000 1.8901 3.6465 -1.7564 15.000 5.3431 3.2239 2.1192 16.000 -0.2742 3.2231 -3.4974 20.000 4.5459 3.1734 1.3726 21.000 1.0247 3.2657 -2.2410 25.000 4.0410 3.0492 0.9917 ~
DDGmichigan
commented
5 years ago Also in the solvent command you added solvent :WAT,C3N
But I want to calculate the interaction energies of C3N molecules so why do I have to include WAT as my solvent?
DDGmichigan
commented
5 years ago Also, now in certain cases, I get this
ACTION OUTPUT: SPAM timing data: TIME: Residue c.o.m. calc: 0.2755 s ( 88.85%) TIME: Peak assignment : 0.0011 s ( 0.37%) TIME: Occupancy calc. : 0.0212 s ( 6.83%) TIME: Energy calc : 0.0012 s ( 0.40%) TIME: Residue reordering : 0.0012 s ( 0.39%) TIME: SPAM Action Total: 0.3100 s TIME: Analyses took 0.0000 seconds.
DATASETS (5 total): GRID "GRID" (float grid), size is 64000000 (256.000 MB) GRID[totalvol] "GRID[totalvol]" (double), size is 1 (0.008 kB) SPAM_00003[DG] "SPAM_00003[DG]" (X-Y mesh), size is 0 SPAM_00003[DH] "SPAM_00003[DH]" (X-Y mesh), size is 0 SPAM_00003[-TDS] "SPAM_00003[-TDS]" (X-Y mesh), size is 0 Total data set memory usage is at least 256.000 MB
DATAFILES (5 total): volmap_C3N.xplor (Xplor File): GRID spam_energies.out (Standard Data File): spam_summary.out (Standard Data File): SPAM_00003[DG] SPAM_00003[DH] SPAM_00003[-TDS] 3kfa_ACN_peak.xyz (Volmap Peaks) info.txt (SPAM info) Warning: File 'spam_energies.out' has no sets containing data. Warning: Set 'SPAM_00003[DG]' contains no data. Warning: Set 'SPAM_00003[DH]' contains no data. Warning: Set 'SPAM_00003[-TDS]' contains no data. Warning: File 'spam_summary.out' has no sets containing data.
To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.
There is no data inside peakfile output and no output in spam_energies.out Any reason for this?
drroe
commented
5 years ago Without seeing the files it's hard to tell. It could be that the coordinates you used when you calculated your peaks (i.e. any centering/rotating/etc that you did) isn't corresponding to the coordinates you're using when running SPAM (i.e. you're not centering/rotating them the same way), so the peaks don't actually correspond to what SPAM expects. Again, I'd need some files to reproduce before I could say for certain.
DDGmichigan
commented
5 years ago Hi Daniel, I can send you the input files and relevant stuff so that you can reproduce the error. The issue I am facing has to do with the values. After having located the hotspots I have used the same x,y,z coordinates in my spam peakfile and the free energies I get is positive for the exact spot where MixMD, SILCS etc methods gave a negative value, even LIE. So I am confused as to what different things may be happening that I do not get favorable energies using SPAM analysis.
DDGmichigan
commented
5 years ago DDGmichigan
commented
5 years ago This contains the prmtop file, the 25 frames of my big traj file, the spam.in file, the MixmD_energies,pdb (these contain the coordinates of the occupancy maxima) i have a small python script which converts the Mixmd_energies.pdb file to a peakfile.xyz
DDGmichigan
commented
5 years ago All I am brainstorming on is how come the energies for the same hotspots become "unfavorable" in SPAM whereas they are favorable interactions when computing using xplor maxima
DDGmichigan
commented
5 years ago again segfault happening
DDGmichigan
commented
5 years ago spam_input file parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/RUNS/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/RUNS/3kfa_md_1-pmemdMPI/3kfa_ACN_production4D.mdcrd 1 2500 1 solvent :C3N,WAT autoimage strip :Na+,Cl- volmap C3N_3kfa.xplor 0.5 0.5 0.5 :C3N@C2 name GRID size 200,200,200 center origin peakcut 0.001 peakfile 3kfa_ACN_peak.xyz run spam 3kfa_ACN_peak.xyz solv C3N reorder cut 10 sphere site_size 6 dgbulk -31.80 dhbulk -18.27 info info.txt summary spam_summary.out out spam_energies.out run
DDGmichigan
commented
5 years ago I really want to get to the bottom of this analysis, why does it segfault ? Any help from you will be super useful Thanks Debarati
drroe
commented
5 years ago After many tries I was finally able to reproduce the segfault. I'll look into it and get back to you ASAP.
DDGmichigan
commented
5 years ago Thanks so much Dan!
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After many tries I was finally able to reproduce the segfault. I'll look into it and get back to you ASAP.
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drroe
commented
5 years ago So the issue is that you have more peaks than residues, and the code wasn't written to handle that case when reordering molecules. I'll have to look at the code a bit more (and maybe consult with the original author) before a fix will be in, but for now try removing the reorder keyword if you don't need it.
drroe
commented
5 years ago @swails it seems to me that reorder should probably be disabled if you have more peaks than solvent residues. There's just no way to guarantee that the same peaks will be occupied any given frame. Am I thinking about this wrong?
DDGmichigan
commented
5 years ago @drroe : Even without the reorder cpptraj gets angry and spits out segfault! I am perplexed why is it giving seg faults when I try to use SPAM analysis!
swails
commented
5 years ago @swails it seems to me that
reordershould probably be disabled if you have more peaks than solvent residues. There's just no way to guarantee that the same peaks will be occupied any given frame. Am I thinking about this wrong?
If the number of water residues is less than the number of peaks (very weird!), then it's impossible to say whether reorder is even possible.
It's closing on 10 years since I wrote any of this code, but here's what I recall:
reorder was added before cpptraj added support for PME energiesHowever, if you have 5 peaks and 3 residues, you obviously can't reorder any molecule into the 4th or 5th peaks. The energy calculations are still well-defined if you do them directly in cpptraj, but I'd be pretty skeptical of simulations where the number of peaks eclipsed the number of solvent molecules. Either you have very little solvent and your system lacks anything resembling 'bulk' behavior or your simulations are unconverged (and probably really unconverged, since solvent 'equilibrates' way faster than large solutes).
drroe
commented
5 years ago Even without the reorder cpptraj gets angry and spits out segfault! I am perplexed why is it giving seg faults when I try to use SPAM analysis!
@DDGmichigan OK, with the files you previously provided I can't reproduce the segfault if reorder is off. Can you provide me the smallest possible test case that causes a segfault with reorder off? If I can reproduce the error there's a chance I can fix it - otherwise I'm stumped.
@swails I'll go ahead and at some point soon disabled reorder when peaks > solvent residues. Thanks.
DDGmichigan
commented
5 years ago @swails Thanks for all your help and suggestions, Thanks to @drroe also for actually trying to help me out on this project. Well, I have just published this paper in May 2019 ' https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.8b00925"
I need to set up SPAM analysis on the systems containing approx 1M acetonitrile+water boxes and get the energies for the hotspots reported in the paper. thats all that I have been trying to set up since last 2 months. Well, I will send the input files and test cases as well, but I still do not understand why I get seg-faults and also "positive energies" for the exact same locations wherein MixMD analysis, SILCS, LIE all generate favorable negative values of interactions
DDGmichigan
commented
5 years ago @swails I do not understand what peakcut should be optimum for my volmap command to generate peak locations as I have approx 450 ACN molecules in 5000 TIP3P waters and a ABL Kinase, no way the peaks could be >> 450 but I get 3000+ peaks if i use peakcut 0.003, how do you define the best possible choice of peakcut in cpptraj? Could I explain where I am getting confused?
DDGmichigan
commented
5 years ago also I am looking for peak locations of my ACN probe and not water peaks.
DDGmichigan
commented
5 years ago As we know that SPAM was originally setup for WATER interaction sites on the protein, when I select solvent C3N, WAT, in my case as its a mixed solvent scenario, will intercations of C3N+water, C3N+protein, C3N with another C3N also be taken into account by the SPAM calculation script or do we have to modify it to take into account all interactions?
jokr91
commented
4 years ago Hi, I just stumbled over this issue and I think I know the reason for this error. As the exception std::bad_alloc is only thrown when the allocation of memory failed, the most likely reason is that you simply ran out of memory. So I do not know the specific code and I do not claim that this is actually the reason, however, it would explain why at one day you get the error and the next day the calculations are running smoothly. It would also explain why @drroe was not able to reproduce the error.
Hope this helps Johannes
drroe
commented
4 years ago @DDGmichigan was there any more progress on this? Was it indeed an out of memory issue?
DDGmichigan
commented
4 years ago Hello Daniel, The spam calculations never worked for me. I used acetonitrile, ethanol, and pyridine, three types of solvent and every time it seg faulted. I can pass on the inputs if you want to check it but I think its only functional with water molecules. I spent like 2-3 months on that and it never worked. Debarati
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@DDGmichiganhttps://github.com/DDGmichigan was there any more progress on this? Was it indeed an out of memory issue?
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drroe
commented
4 years ago I can pass on the inputs if you want to check it but I think its only functional with water molecules.
Anything you can provide would be helpful. Topologies/coordinates/input to reproduce the problem will go a long way to helping me figure out what is going wrong.
DDGmichigan
commented
4 years ago Sure Let me create a folder and I shall send you the topologies, the input file and the trajectory to help reproduce the problem I face. So to give a small background, I have recently worked on co-solvent based simulations to detect binding sites on kinases. Publication info https://pubs.acs.org/doi/full/10.1021/acs.jcim.8b00925
Once you quickly scan through the paper, you will see we detect 4-5 hotspots on kinases based on the mixMD simulation probe occupancy.
So, what I expected out of SPAM analyses was, is there a way I can provide it the x,y,z coordinates of the hotspot locations and get a ~estimate of the free energy of binding associated with a probe molecule to the kinase site. THIS was my goal. I will create a folder and provide you the input files so that it might help us figure out what may be wrong. Thanks Daniel for spending time on this. I really appreciate. Regards Debarati
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I can pass on the inputs if you want to check it but I think its only functional with water molecules.
Anything you can provide would be helpful. Topologies/coordinates/input to reproduce the problem will go a long way to helping me figure out what is going wrong.
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DDGmichigan
commented
4 years ago Sent the traj zipped file using my personal gmail account buri2211@gmail.com Let me know if you get the zipped traj file Debarati
DDGmichigan
commented
4 years ago We need to tell the SPAM module explicitly that solvent of interest is ACN (my acetonitriles) and not WAT If that can be done clearly, I guess we can get meaningful interaction energies for these small co-solvent probes.
drroe
commented
4 years ago OK, I've made some progress. The segfault was being caused by the occasional extremely large energy observed for a peak. When determining the number of bins for the histogram to do the SPAM energy calculation (equation 2 in original Cui/Swails/Manas SPAM paper) the large energy would lead to the number of bins overflowing and becoming negative, which lead to the segfault. I've got a check in place for that now in a branch I'm working on, but I'm going to dig a little deeper and see if those energies are "real" or are part of another bug.
@DDGmichigan thanks for the files, they are helping me diagnose and fix this.
DDGmichigan
commented
4 years ago Hi Dan, Your most welcome. Its you who is helping me dig deep as to why are the energies sometimes positive numbers even though they should be negative, as validated by LIE and our Mixmd free energy calculations. Please let me know if you need more files/inputs/crd files anything even the free energy script I can provide anything that can help remedy the problem. Thanks Debarati
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OK, I've made some progress. The segfault was being caused by the occasional extremely large energy observed for a peak. When determining the number of bins for the histogram to do the SPAM energy calculation (equation 2 in original Cui/Swails/Manas SPAM paper) the large energy would lead to the number of bins overflowing and becoming negative, which lead to the segfault. I've got a check in place for that now in a branch I'm working on, but I'm going to dig a little deeper and see if those energies are "real" or are part of another bug.
@DDGmichiganhttps://github.com/DDGmichigan thanks for the files, they are helping me diagnose and fix this.
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DDGmichigan
commented
4 years ago Hello Daniel, Any luck with the SPAM error? Thanks Debarati
drroe
commented
4 years ago Yes, I'm still working on that branch. I haven't committed yet because I'm also working on some speed improvements for the volmap command (around 1.3 to 1.5x faster right now). Also, the "peaks" data from volmap will be a dataset so you will be able to do volmap + spam in the same run. Hope to have it in by this week.
DDGmichigan
commented
4 years ago Thanks so much. I did not want to bug you with this as I know you may be busy with several projects. Thanks though for looking into this. Regards Deb
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Yes, I'm still working on that branch. I haven't committed yet because I'm also working on some speed improvements for the volmap command (around 1.3 to 1.5x faster right now). Also, the "peaks" data from volmap will be a dataset so you will be able to do volmap + spam in the same run. Hope to have it in by this week.
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DDGmichigan
commented
4 years ago @drroe Could you decipher the bug in the SPAM calculations? Thanks! Debarati
DDGmichigan
commented
4 years ago @drroe I realized I get same errors with other probe solvents I used ( isopropanol, pyridine, imidazole, n-methyl acetamide)...!
DDGmichigan
commented
4 years ago Hello Daniel, Were you able to find the root cause for the segmentation fault error? Also last time you mentioned a speed-up on volmap command, hows that evolving? I am excited to apply this recent updated volmap to extract peaks from my cosolvent simulations and do a free energy analysis with SPAM!
Sorry for bugging up with SPAM! Regards Debarati
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Yes, I'm still working on that branch. I haven't committed yet because I'm also working on some speed improvements for the volmap command (around 1.3 to 1.5x faster right now). Also, the "peaks" data from volmap will be a dataset so you will be able to do volmap + spam in the same run. Hope to have it in by this week.
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drroe
commented
4 years ago OK - so the volmap stuff is close but not ready for prime time yet. So I'm going to split off the SPAM fixes into a different branch and try to merge that today so you can at least start using that.
drroe
commented
4 years ago Once #838 passes I will merge it and you should be good to go.
DDGmichigan
commented
4 years ago @drroe Thanks so much for tackling these SPAM issues..Really appreciate it Daniel. Regards
drroe
commented
4 years ago @DDGmichigan OK, changes are merged in. Give it a try and let me know how it goes.
I am using spam to calculate free energies for a mixed solvent MD simulation (protein is ABL kinase) My input file is as follows: parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_2pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_2pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_3pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_3pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_4pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_4pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_5pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_5pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_6pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_6pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_7pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_7pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_8pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_8pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_10pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_10pmemdcuda/New4H_production.1.crd 1 50 1
Center and process image
center :1-286 mass origin
image origin familiar com :1-286
# autoimage
Align trajectory to reference structure by minimizing RMSD
reference /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/setup_solvbox/3kfa_layer_ACN_H2O_5-95vv.pdb strip :Cl-,Na+ rms reference mass out 3kfa_ACN_15-20ns_md_CA_rmsd.txt :1-286@CA spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -30.3 dhbulk -22.2 info info.txt summary spam_summary.out out spam_energies.out
Error I get is:
Read 1000 frames and processed 1000 frames. TIME: Avg. throughput= 16.8114 frames / second.
ACTION OUTPUT: SPAM timing data: TIME: Residue c.o.m. calc: 0.0058 s ( 0.02%) TIME: Peak assignment : 0.0196 s ( 0.07%) TIME: Occupancy calc. : 0.0013 s ( 0.00%) TIME: Energy calc : 27.4013 s ( 99.89%) TIME: Residue reordering : 0.0040 s ( 0.01%) TIME: SPAM Action Total: 27.4324 s terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)