Re: [gmx-users] Define intermolecular interactions in L-J simulation

Den 2019-10-23 kl. 18:22, skrev Li, Shi: Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A

[gmx-users] QM/MM run tips or tutorials

Hi all, I would like to try Gromacs 2018 with QM. I am good enough with running MD on Gromacs, but have never used QM. Any tips how to get started or any links to tutorials will be very helpful. Best regards, Vlad -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Define intermolecular interactions in L-J simulation

On 10/23/19 12:22 PM, Li, Shi wrote: Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A

[gmx-users] Define intermolecular interactions in L-J simulation

Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

On 10/22/19 12:04 AM, Amit Jaiswal wrote: Dear Jorden, Thanks for your reply. As you have suggested, i found there is a mismatch of the atom number in the zn.itp file and the .gro file. I have included few residues of .gro file for your convenience. What i understand is that I have to

Re: [gmx-users] regression test errors

Thanks a lot Paul. best regards, D On Wed, Oct 23, 2019 at 4:44 AM Paul bauer wrote: > Hello Dave, > > I thought it was something like that. > The error is harmless (just telling you that MPI is doing its job), and > the testing script gets confused because of the extra message in the > output

Re: [gmx-users] regression test errors

Hello Dave, I thought it was something like that. The error is harmless (just telling you that MPI is doing its job), and the testing script gets confused because of the extra message in the output file. So I think you are good to go (and we need to do something about the testing script).

Re: [gmx-users] regression test errors

Hi Paul, I checked using this command for a specific folder, and I used '-mpirun mdrun' rather '-mpirun mpirun': ./gmxtest.pl -mpirun mdrun -np 2 -noverbose rotation I get lot of these errors: topol.tpr file different from ./reference_s.tpr. Check files in flex for flex FAILED. Check

Re: [gmx-users] regression test errors

Hello Dave, this is weird, no idea why it didn't work then. You can try running the test suite manually in the folder you found with perl gmxtest.pl -mpirun mpirun -np X -noverbose That will show if the test binary works and should report any failing tests. Don't forget to source the GMXRC

Re: [gmx-users] regression test errors

Hi Paul, Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now. Regarding tests, I found the folder here build/tests/regressiontests So I checked all the log using a simple script (searching keyword 'Finished') and it shows that all the log files have Finished properly in their corresponding

Re: [gmx-users] regression test errors

Hello Dave, You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a MPI enabled build of GROMACS. This is what the error message tries to tell you, but we might need to improve on this. There should be a regressiontests folder somewhere in your build tree if it downloaded the

Re: [gmx-users] regression test errors

Hi Paul, Thanks for your reply. a) I just checked there is no tests/regressiontests, some other folder is there test/sphysicalvalidation There is no log file. b) Regarding thread-mpi I think it is not installed because when I use some command like this: gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0

Re: [gmx-users] regression test errors

Hello Dave, Did you have a look into the log files from the regression tests under tests/regressiontests? They might give us some insight into what is happening. The warning in respect to thread-MPI is harmless, it just tells you that you are using real MPI instead of thread-MPI. Cheers Paul

Re: [gmx-users] Solvation of protein on membrane surface

Thanks a lot for your help. ‫בתאריך יום ב׳, 21 באוק׳ 2019 ב-19:51 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu ‬‏>:‬ > > > On 10/20/19 5:57 AM, Olga Press wrote: > > Prof. Lemkul, > > Thank you very much for your reply. I would be very grateful if you can > > help me with some questions regarding