Closed lukhman9020 closed 4 months ago
maisebastian
commented
5 months ago Dear lukhman9020, it looks like you have provided in the MOLCAS.qmmm.table file only information about the QM region. Note that you need to provide also information for the MM atoms (atom type info and connectivity) in the same way for all MM atoms, because only with this information can the MM energy be computed.
Best, Sebastian
lukhman9020
commented
5 months ago Dear lukhman9020, it looks like you have provided in the MOLCAS.qmmm.table file only information about the QM region. Note that you need to provide also information for the MM atoms (atom type info and connectivity) in the same way for all MM atoms, because only with this information can the MM energy be computed.
Best, Sebastian
Dear Sir, Thank you for your reply. It is challenging to manually provide atom type information and connectivity details for 22-5046 atoms. If you are aware of a more efficient method, could you please assist me in this task?
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
5 months ago Dear lukhman9020, your MM region consists simply of a large number of water molecules, so the MM part is easily scriptable. It should look like this:
22 O x y z 63 23 24
23 H x y z 64 22
24 H x y z 64 22
25 O x y z 63 26 27
26 H x y z 64 25
27 H x y z 64 25
3i+28 O x y z 63 3i+29 3i+30
3i+29 H x y z 64 3i+28
3i+30 H x y z 64 3i+28
...You can write a simple Python (or similar) script that takes your geometry file and produces the content of the table file.
Best, Sebastian
lukhman9020
commented
5 months ago Dear lukhman9020, your MM region consists simply of a large number of water molecules, so the MM part is easily scriptable. It should look like this:
22 O x y z 63 23 24 23 H x y z 64 22 24 H x y z 64 22 25 O x y z 63 26 27 26 H x y z 64 25 27 H x y z 64 25 3i+28 O x y z 63 3i+29 3i+30 3i+29 H x y z 64 3i+28 3i+30 H x y z 64 3i+28 ...You can write a simple Python (or similar) script that takes your geometry file and produces the content of the table file.
Best, Sebastian
OK, Thank you sir.
lukhman9020
commented
5 months ago Dear lukhman9020, your MM region consists simply of a large number of water molecules, so the MM part is easily scriptable. It should look like this:
22 O x y z 63 23 24 23 H x y z 64 22 24 H x y z 64 22 25 O x y z 63 26 27 26 H x y z 64 25 27 H x y z 64 25 3i+28 O x y z 63 3i+29 3i+30 3i+29 H x y z 64 3i+28 3i+30 H x y z 64 3i+28 ...You can write a simple Python (or similar) script that takes your geometry file and produces the content of the table file.
Best, Sebastian
Dear Sir, I hope this email finds you well. I recently updated the MOLCAS.qmmm.table in my QM/MM system, but unfortunately, the calculation has come to a halt. Interestingly, after the update, there is no information in my QM.error file. I'm reaching out for your guidance and assistance in resolving this matter. I've noticed that the TINKER software isn't installed in the openmolcas folder but rather outside it. Could this be the cause of the problem?. I here attach my new MOLCAS.qmmm.table and qm.log files
https://drive.google.com/drive/folders/1TvYGnfixAm-5FU4uc0plxyZVyMaqG5CT
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago The QM.log file shows that the Molcas calculation terminated with exit code 250. You need to check the Molcas log file to see what went wrong.
lukhman9020
commented
4 months ago The QM.log file shows that the Molcas calculation terminated with exit code 250. You need to check the Molcas log file to see what went wrong.
Thank you sir, I will check.
lukhman9020
commented
4 months ago The QM.log file shows that the Molcas calculation terminated with exit code 250. You need to check the Molcas log file to see what went wrong.
Dear Sir,
I hope this message finds you well. While analyzing the molcas.out file in the scratch directory, I encountered an error like this
"
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
&GATEWAY
only a single process is used
available to each process: 500 MB of memory, 1 thread?
pid: 116352()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
TINKER keyword found, run /home/mhgroup1/tinker///tkr2qm_s MOLCAS.xyz>MOLCAS.Tinker.log ############################################################################### ###############################################################################
############################################################################### ############################################################################### --- Stop Module: gateway at Mon Feb 5 13:34:15 2024 /rc=-6 --- --- Module gateway spent 7 seconds ---
.########################. .# Non-zero return code #. .########################.
Timing: Wall=7.61 User=0.07 System=0.04" Additionally, the Molcas.log file is absent in both the scratch and calculation running folder (ICOND_00000). Please advise on resolving these issues.
I here attach the files are present in scratch folder https://drive.google.com/drive/folders/1BPGoxKGxHuZg-nWDD3Ous7L6G6gMvUTp
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago It seems that tinker did not run correctly. This can most easily be trouble-shooted if you go into the scratch directory, load the necessary OpenMolcas environment variables, and then try to run /home/mhgroup1/tinker/tkr2qm_s If the program does not run, first check ldd /home/mhgroup1/tinker/tkr2qm_s to see which libraries might be missing. Considering that there seems to be no MOLCAS.Tinker.log file, it seems that the issue is with running tinker and not with the input files for tinker.
lukhman9020
commented
4 months ago It seems that tinker did not run correctly. This can most easily be trouble-shooted if you go into the scratch directory, load the necessary OpenMolcas environment variables, and then try to run /home/mhgroup1/tinker/tkr2qm_s If the program does not run, first check ldd /home/mhgroup1/tinker/tkr2qm_s to see which libraries might be missing. Considering that there seems to be no MOLCAS.Tinker.log file, it seems that the issue is with running tinker and not with the input files for tinker.
Dear Sir, Thank you for your reply. I hope this message finds you well. Upon checking the Tinker directory, I found only three directories: lib, fftw, and bin. Despite thorough searches, I couldn't locate the 'tkr2qm_s' in each directories. I think The installation seems incomplete, although I can access the Tinker interface via 'xyzedit.' The Tinker manual lacks guidance on setting up these libraries. Could you please provide detailed instructions on resolving this issue and installing the missing libraries?
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago lukhman9020
commented
4 months ago Thank you sir.
lukhman9020
commented
4 months ago Dear Sir, I hope this message finds you well. I am currently encountering an error while executing a Molcas-Tinker calculations (ICOND_00000/run.sh). In the QM.log file, I received the following error message: "
Starting the job execution START: /home/mhgroup1/PKLu/DHICA/t/ICOND_00000/master 2024-02-08 00:06:59.172733 "/home/mhgroup1/kumar/OpenMolcas23.06//bin/pymolcas MOLCAS.input" FINISH: /home/mhgroup1/PKLu/DHICA/t/ICOND_00000/master 2024-02-08 00:06:59.647325 Runtime: 0:00:00.474592 Error Code: 112 File /home/mhgroup1/PKLu/DHICA/t/ICOND_00000/master/MOLCAS.1.JobIph not found, cannot move to savedir! "
Additionally, in the molcas.out file, I received an error
" ()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
&GATEWAY
only a single process is used
available to each process: 500 MB of memory, 1 thread?
pid: 1265231()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
TINKER keyword found, run /home/mhgroup1/kumar/OpenMolcas23.06/tinker-6.3.3/bin/tkr2qm_s MOLCAS.xyz>MOLCAS.Tinker.log File Molcas -1 0 not found! --- Stop Module: gateway at Thu Feb 8 00:06:59 2024 /rc=_RC_INPUTERROR ---
.####################. .# User input error #. .####################.
Timing: Wall=0.28 User=0.03 System=0.04" Could you please assist me in resolving this issue at your earliest convenience?
I here attach all files are present in ICOND_00000 and scratch directory https://drive.google.com/drive/folders/1u8fUxuE4uH_W1nQMSA2M6LlAIoyxGMuI
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago Please check that your MOLCAS.qmmm.key file looks similar to the example file here: https://github.com/sharc-md/sharc/blob/main/examples/SHARC_MOLCAS_tinker/MOLCAS.qmmm.key
In particular, the lines specifying the atoms should have no leading white space. If there is leading white space, then the "QM" and "MM" lines will not be read correctly and then the interface does not know the number of QM and MM atoms.
lukhman9020
commented
4 months ago Please check that your MOLCAS.qmmm.key file looks similar to the example file here: https://github.com/sharc-md/sharc/blob/main/examples/SHARC_MOLCAS_tinker/MOLCAS.qmmm.key
In particular, the lines specifying the atoms should have no leading white space. If there is leading white space, then the "QM" and "MM" lines will not be read correctly and then the interface does not know the number of QM and MM atoms.
Ok, Thank you sir. I will check .
lukhman9020
commented
4 months ago Please check that your MOLCAS.qmmm.key file looks similar to the example file here: https://github.com/sharc-md/sharc/blob/main/examples/SHARC_MOLCAS_tinker/MOLCAS.qmmm.key In particular, the lines specifying the atoms should have no leading white space. If there is leading white space, then the "QM" and "MM" lines will not be read correctly and then the interface does not know the number of QM and MM atoms.
Ok, Thank you sir. I will check .
Dear Sir, I hope this message finds you well. I am writing to seek urgent assistance with resolving an error encountered during a QM/MM calculation. I have reviewed my MOLCAS.qmmm.key and QM.in files, ensuring they match the references provided. Additionally, I included "GRAD 1 2 3" in the QM.in file. However, the calculation halts, and I'm unable to proceed. While running the calculation, I encountered the following error message in the MOLCAS.Tinker.log file: " This is a QM/MM calculation
QMMMSETUP -- Wrong NbInQM value **
TINKER is Unable to Continue; Terminating the Current Calculation " From my understanding, this error seems to be related to specifying the number of atoms belonging to the QM region in the &QMMSETUP section. But I don't know how to solve this. Could you please provide guidance on how to correct this error? Any assistance or insights you can offer would be greatly appreciated. I here attach the files are present in my Scratch, ICOND_00000 directory and also MOLCAS.input file which is used for creating Molcas.template. https://drive.google.com/drive/folders/1u8fUxuE4uH_W1nQMSA2M6LlAIoyxGMuI
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago One possible mistake I could spot is the path to the force field file in the key file:
parameters home/mhgroup1/kumar/OpenMolcas23.06/tinker-6.3.3/params/oplsaa.prm
QMMM 5046
QM -1 21
MM -22 5046
QMMM-ELECTROSTATICS ESPFI assume that the path should start with a slash ( /home/...). Please check.
lukhman9020
commented
4 months ago One possible mistake I could spot is the path to the force field file in the key file:
parameters home/mhgroup1/kumar/OpenMolcas23.06/tinker-6.3.3/params/oplsaa.prm QMMM 5046 QM -1 21 MM -22 5046 QMMM-ELECTROSTATICS ESPFI assume that the path should start with a slash ( /home/...). Please check.
Dear sir, I tried. But I got same error.
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.
maisebastian
commented
4 months ago It appears that most problems you are facing with the calculation are related to some hard-coded limits in OpenMolcas. There are at least two variables, called "Mxdbsc" and "Mxdc". Both can lead to errors if you employ too many point charges in your calculation. As described in the OpenMolcas forum (https://molcasforum.univie.ac.at/viewtopic.php?id=932, https://molcasforum.univie.ac.at/viewtopic.php?id=190), one can increase these if you have the OpenMolcas source code and can recompile it. You would need to set mxAtom to more than your number of atoms, and Mxdbsc to some large value (but I do not know how large).
If you do not have this possibility, the only solution is to reduce the number of water molecules. The limit for Mxdc is apprently 5000 in recent OpenMolcas versions, so removing 16 water molecules would be enough. I was able to finish the calculation with an adapted OpenMolcas installation that has a higher limit for Mxdbsc. But with a standard v23.06 installation (like you used), the error related to Mxdbsc will persist. In https://gitlab.com/Molcas/OpenMolcas/-/blob/master/src/Include/Molcas.fh, this value is 1000, but you will have to test how many water molecules you can use. If this would be not enough, your only chance is to increase the parameters and recompile OpenMolcas.
Best, Sebastian
Note: The files that you sent me in the last Google Drive link do work. I was able to finish such a calculation with a recompiled OpenMolcas version and 4998 atoms.
lukhman9020
commented
4 months ago It appears that most problems you are facing with the calculation are related to some hard-coded limits in OpenMolcas. There are at least two variables, called "Mxdbsc" and "Mxdc". Both can lead to errors if you employ too many point charges in your calculation. As described in the OpenMolcas forum (https://molcasforum.univie.ac.at/viewtopic.php?id=932, https://molcasforum.univie.ac.at/viewtopic.php?id=190), one can increase these if you have the OpenMolcas source code and can recompile it. You would need to set mxAtom to more than your number of atoms, and Mxdbsc to some large value (but I do not know how large).
If you do not have this possibility, the only solution is to reduce the number of water molecules. The limit for Mxdc is apprently 5000 in recent OpenMolcas versions, so removing 16 water molecules would be enough. I was able to finish the calculation with an adapted OpenMolcas installation that has a higher limit for Mxdbsc. But with a standard v23.06 installation (like you used), the error related to Mxdbsc will persist. In https://gitlab.com/Molcas/OpenMolcas/-/blob/master/src/Include/Molcas.fh, this value is 1000, but you will have to test how many water molecules you can use. If this would be not enough, your only chance is to increase the parameters and recompile OpenMolcas.
Best, Sebastian
Note: The files that you sent me in the last Google Drive link do work. I was able to finish such a calculation with a recompiled OpenMolcas version and 4998 atoms.
Thank you very much for your help.
Dear Sir, I hope this message finds you well. I am encountering an issue while running Molcas calculations. After successfully generating 600 snapshots, re-imaging the files, and converting them to .rst7 format, I selected 550 snapshots for a SHARC simulation. Subsequently, I used the "SHARC/amber_to_initconds.py" script to generate initiconds files. However, when attempting to run the Molcas-Tinker calculations (ICOND_00000/run.sh), I encountered the following error in the Qm.err file: Traceback (most recent call last): " File "/home/mhgroup1/kumar/sharc/bin/SHARC_MOLCAS.py", line 3560, in run_calc setupWORKDIR(WORKDIR, Tasks, QMin) File "/home/mhgroup1/kumar/sharc/bin/SHARC_MOLCAS.py", line 3175, in setupWORKDIR geomstring = writegeomfile(QMin) File "/home/mhgroup1/kumar/sharc/bin/SHARC_MOLCAS.py", line 3134, in writegeomfile tmpline = geomtemplate[iatom + 1].split() IndexError: list index out of range " especially molcas.out files are not being formed in the scratch directory during the execution of ICOND_00000/run.sh. I have attached relevant files (MOLCAS.1.RasOrb.init, MOLCAS.qmmm.table, QM.err, run.sh, MOLCAS.3.RasOrb.init, MOLCAS.resources, QM.in, MOLCAS.qmmm.key, MOLCAS.template, QM.log) for your reference.
https://drive.google.com/drive/folders/1W0M-Ub7yd4na0Qz8ivLW4aGGnTQVPt9d?usp=sharing
Looking forward to your guidance.
Best regards, LUKHMANUL HAKEEM K.