[gmx-users] Residue id of capped peptide getting changed when adding molecules

Hi, I have a capped peptide (ACE-ALA-NME) and now when i add the other molecules through the command "gmx insert-molecules", the residue id of the capped peptide, which was 1 as: 1ACECH3 1ACE HH31 1ACE HH32 1ACE HH33 1ACE C 1ACE O 1ALA N

[gmx-users] xpm2ps

Hello everyone When I use xpm2ps in Gromacs 2018.3 and open .eps file, I see that a balck line cover the numbers in y and x axis. Any person can help me?! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Setting rcon according to system

Hi, On Wed, Nov 14, 2018 at 3:18 AM Sergio Perez wrote: > Hello, > First of all thanks for the help :) > I don't necessarily need to run it with 100 processors, I just want to know > how much I can reduce rcon taking into account the knowledge of my system > without compromising the accuracy.

Re: [gmx-users] Running GPU issue

Hi, I expect that that warning is fine (for now). The error you saw is clear evidence of a bug. There's a few things you might try to help narrow things down. * Is the error reproducible on each run of mdrun? * 2018.3 was not designed or tested on CUDA 10, which was released rather later. If you

Re: [gmx-users] Running GPU issue

I forgot to add. While compiling gromacs I got following error at the very beggining: [ 3%] Built target gpu_utilstest_cuda /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu: In function ?int do_sanity_checks(int, cudaDeviceProp*)?:

Re: [gmx-users] Running GPU issue

Mark, Thank you. Then I have an issue I can not find a way to solve. My MD using GPU fails at the very beginning while CPU-only MD runs no problem with the same tpr file. I can not find what "HtoD cudaMemcpyAsync failed: invalid argument" means. Here is some diagnostics. $ uname -a Linux

Re: [gmx-users] pcoupl Berendsen

On 11/14/18 5:28 AM, Gonzalez Fernandez, Cristina wrote: Hi Justin, I have taken a few days in answering you because I was trying to reduce the discrepancies between the pressure I obtain after simulation and the one I set in the .mdp file. However, I have no achieve very good results. As I

Re: [gmx-users] NPT not working

On 11/14/18 6:07 AM, Hanin Omar wrote: Thank you Justin for your answer, i went back to my system and did all sort of tests, and the system works fine without the RDC restraint. Since the RDC values where used to generate the original pdb file of the protein i think the strongest option

Re: [gmx-users] how to keep the ligand inside water box

On 11/14/18 7:08 AM, Rahma Dahmani wrote: Hi GMX users, After running nvt equilibration, my ligand get out the box and before proceeding to npt equilibration i want to know how to get (and keep if is it possible) the ligand in water box* center* ? There is no reason to do this. In a

Re: [gmx-users] how to keep the ligand inside water box

Hi, I don't know if there any way to keep ligand in the center of box but I think you should apply the *position restraint* on the ligand in the equilibrium process if you don't want the ligand move significantly On Wed, Nov 14, 2018 at 1:08 PM Rahma Dahmani wrote: > Hi GMX users, > > After

[gmx-users] how to keep the ligand inside water box

Hi GMX users, After running nvt equilibration, my ligand get out the box and before proceeding to npt equilibration i want to know how to get (and keep if is it possible) the ligand in water box* center* ? Thank you ! -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche:

Re: [gmx-users] NPT not working

Thank you Justin for your answer, i went back to my system and did all sort of tests, and the system works fine without the RDC restraint. Since the RDC values where used to generate the original pdb file of the protein i think the strongest option would be to say that i have an issue with the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 40

Dear Justin Thanks for your reply Yes I edited the topology and resolved the problem Best Farial On Tue, Nov 13, 2018 at 3:34 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to >

Re: [gmx-users] Lincs warning

Dear Mark Thank you for your reply I resolved my problem by refining the output ot the tool Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] pcoupl Berendsen

Hi Justin, I have taken a few days in answering you because I was trying to reduce the discrepancies between the pressure I obtain after simulation and the one I set in the .mdp file. However, I have no achieve very good results. As I indicated in the previous email, in my simulations

Re: [gmx-users] Setting rcon according to system

Hello, First of all thanks for the help :) I don't necessarily need to run it with 100 processors, I just want to know how much I can reduce rcon taking into account the knowledge of my system without compromising the accuracy. Let me give some more details of my system. The system is a sodium