Re: [gmx-users] Failed tests, need help in troubleshooting

Hi Cameron, I meant any log file from a run with the hardware + software combination. The log file contains hardware and software detection output that is useful in identifying issues. Do the unit tests pass? -- Szilárd On Tue, Apr 23, 2019 at 12:38 PM Cameron Fletcher (CF) <

Re: [gmx-users] Failed tests, need help in troubleshooting

Hello Szilárd, Do you mean log files created in each regression test? On 23/04/19 3:43 PM, Szilárd Páll wrote: > What is the hardware you are running this on? Can you share a log file, > please? > -- > Szilárd > > > On Mon, Apr 22, 2019 at 9:24 AM Cameron Fletcher (CF) < >

Re: [gmx-users] Failed tests, need help in troubleshooting

What is the hardware you are running this on? Can you share a log file, please? -- Szilárd On Mon, Apr 22, 2019 at 9:24 AM Cameron Fletcher (CF) < circumf...@disroot.org> wrote: > Hello, > > I have installed gromacs 2019.1 on CentOS 7.6 . > While running regressions tests 2019.1 certain tests

Re: [gmx-users] SASA calculation for one replica in REMD

Check gmx sasa -h It is implemented in Gromacs On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible

Re: [gmx-users] SASA calculation for one replica in REMD

Hi, I don't know if sasa calculations are implemented in gromacs. But if you know a little bit of Python you can use MDTraj for that: http://mdtraj.org/latest/examples/solvent-accessible-surface-area.html or also Pymol: https://pymolwiki.org/index.php/Get_Area Cheers, Simone Il mar 23 apr

[gmx-users] SASA calculation for one replica in REMD

Dear Gromacs Users, I did replica exchange molecular dynamics simulation which contains 25 replicas. Now I want to calculate the solvent accessible surface area of the surfactant (the first replica in my REMD) I used in my simulation at 298 K. How can I do that? Can anyone help me? Thank you.

Re: [gmx-users] Removing periodic boundary conditions on a dimer

HI, I actually just did it after posting this post and the two monomers appeared to be good (no separated) but the ligand is on the opposite site and when I tried to center nothing happen. Le mar. 23 avr. 2019 à 10:54, Simone Orioli a écrit : > Hi, > Have you tried the following? It usually

Re: [gmx-users] Removing periodic boundary conditions on a dimer

Hi, Have you tried the following? It usually worked for me, but I used to run simulations on old versions of Gromacs so it might be deprecated. trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol Il mar 23 apr 2019, 10:51 Nawel Mele ha scritto: > Dear Gromacs users, > > I have a

[gmx-users] Removing periodic boundary conditions on a dimer

Dear Gromacs users, I have a dimer system with a ligand in one of the monomer. I am trying to remove the periodic boundary conditions to visualise my simulation but whatever steps I used the monomers don't want to be centered in the box. I tried these steps using a custom index file corresponding

Re: [gmx-users] increase membrane dimensions

thank you John for your help, I solved using gmx genconf and the KALP15 tutorial, charm gui also worked, but I preferred to use gromos ff Emiliano On 2019-04-16 17:48, John Whittaker wrote: Sorry for the double post, but you could also try using CHARMM-GUI. http://www.charmm-gui.org/

[gmx-users] Multiple MD simulation

Dear all, I have done the long 200ns MD simulation of protein in water. I have received a comment from the reviewer that for the convergence of the results I have to perform multiple simulations using different initial conformations. Can anyone tell me the criteria for taking the different initial