[gmx-users] surface energy for polymer boxes

Dear users, I have a question. I simulated different box with a polymer (PVDF) and water/salt (NaCl) solution. I would like to know if there's a method to calculate a value of a surface energy of my polymer. I tried to use the command gmx energy for the calculation of the surface tension, after

Re: [gmx-users] Frozen group moves!

Den 2019-10-21 kl. 21:24, skrev Alex: Dear all, I freeze a group in my system in all directions as normal: freezegrps = GR freezedim= Y Y Y So, I was expecting that the coordinates and velocities do not get updated during the simulation, however, here is just part

Re: [gmx-users] Frozen group moves!

Hi, Thanks for the response. On Tue, Oct 22, 2019 at 02:04 David van der Spoel wrote: > Den 2019-10-21 kl. 21:24, skrev Alex: > > Dear all, > > I freeze a group in my system in all directions as normal: > > freezegrps = GR > > freezedim= Y Y Y > > So, I was

Re: [gmx-users] Fatal error: no domain decomposition

Hi Justin, thanks a lot. I followed the link and modify rcon accordingly. The problem was fixed. Thank you once again. Cheers, /P El sáb., 19 oct. 2019 a las 16:34, Justin Lemkul () escribió: > > > On 10/18/19 6:35 AM, Patricia Saenz Méndez wrote: > > Hi! > > I am trying to run a simple MD

[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] supercell

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-genconf.html ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

Re: [gmx-users] setting up osmotic gradient across bilayer.

Your system has a periodic boundary condition applied, so if you have a single bilayer then all the water is part of the same water pool. So what you observed is entirely consistent with the expected behaviour; removing some waters leaves a void, which the remaining waters will then move to fill.

Re: [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.

Hi, Can you please file an issue on redmine.gromacs.org with the description you gave here? Thanks, -- Szilárd On Thu, Oct 17, 2019 at 5:01 PM Artem Shekhovtsov wrote: > Hello! > Problem: The launch of mdrun that does not require video cards exit with > fatal error if at least one video card

[gmx-users] setting up osmotic gradient across bilayer.

Hello users I am trying to check water transport through a membrane protein. I ran simulation for 10 ns. In first attempt I couldn't see significant transport through protein although pore was filled. I hypothesized it could be due to osmotic equilibrium. so in my next mdrun I deleted all water

Re: [gmx-users] GROMACS showing error

Hi, Please direct GROMACS usage questions to the users' list. Replying there, make sure you are subscribed and continue the conversation there. The issue is that you requested static library detection, but the hwloc library dependencies are not correctly added to the GROMACS link dependencies.

[gmx-users] supercell

Dear all, I have a gromacs trajectory for which I need to generate supercell of its last 5ns. The supercell needs to be two times larger than the initial cell from each side. I wonder if there is a tools available in gromacs for doing that? Regards, Alex -- Gromacs Users mailing list * Please

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

Dear Amit, Yes, you need to correct the atom number in the "zn.itp" file in your case. >From your co-ordinate file, it is clear that in order to restrain Zn atom you need to put restraint potential on atom number corresponding to Zn atom which is 4265 in your case instead of 2220. I think this

Re: [gmx-users] regression test errors

Hi All, Any hints/help much appreciated why am getting regression tests failure. Also to mention I think thread-mpi was not installed as I got an error saying "MPI is not compatible with thread-MPI. Disabling thread-MPI". How to check the compatibility? Thanks. best regards, D On Sun, Oct 20,