[gmx-users] Tabulate potential

Dear All, I am reading up about the tabulation table. I was wondering, how does GROMACS deal with periodic structure when the table is tabulated since PME still not available in my version? Also is the new version of GROMACS can do user-PME? Thank you very much. Best regards, Ben -- Gromacs

Re: [gmx-users] Turning off electrostatic between molecules

ory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Tam, Benjamin Sent: Monday, August 12, 2019 7:38:51 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [EXTERNAL] [gmx-users] Turning off electrostat

[gmx-users] Turning off electrostatic between molecules

Dear All, I am thinking of a way to simulate a porous system where the gases are very diluted. I would like to add more molecules into the system in order to increase the statistic but would like to turn off molecules - molecules electrostatic interaction. I understand there are ways to turn

Re: [gmx-users] Pressure coupling problem

I’ll also ask, do you actually need a barostat, or will NVT be fine? Or are there ways to relax your system to an appropriate density without seeing the problem behavior? Best, Jacob On May 23, 2019, at 10:23 AM, Tam, Benjamin mailto:benjamin.tam...@ucl.ac.uk>> wrote: Dear all, T

Re: [gmx-users] Pressure coupling problem

of bug in the newer version or am I missing something? Best, Ben -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Tam, Benjamin Sent: 23 May 2019 11:40 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pressure coupling problem Dear

[gmx-users] Pressure coupling problem

Dear Gromacs user, Currently, I am baffled about a simulation that I am running and I hope I will find some answer here. Initially, I have run my system with Berendsen barostat to equilibrate for 1 ns. The system looks fine as there is no box explosion. However, after the equilibration, I

[gmx-users] Central atom for improper dihedral

Dear gromacs user, For the improper dihedral function type 4, when writing in [ dihedraltypes ], which position in the naming is the central atoms? Thank you very much. Best regards, Ben -- Gromacs Users mailing list * Please search the archive at

[gmx-users] graphene wall piston acceleration simulation

Dear Gromacs-User, I have a question regarding graphene wall piston simulation. As far as I understand, a constant acceleration/force is applied onto the graphene wall at x direction when I put acceleration = 0.1 0.0 0.0 . However when I look at the movie, it seems to have sudden jerk movement

Re: [gmx-users] Problems with large molecule simulation

Hi Justin, Thank you for replying, the problem is this: Fatal error: Atomtype Zr110418 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors because the number and the name combine together i.e. supposed to

Re: [gmx-users] Problems with large molecule simulation

Dear gromacs user, I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count: 2MOL C2 9998 3.987 2.259 6.276 2MOL C5 3.987 2.061 6.079 2MOL C11