[gmx-users] Ion pair

Hi everybody, I am working with electrolytes simulations using Gromacs, so I am trying to get the residence time (ion pair lifetime, ion cage lifetime) of the ions. I tried to use gmx hbond with the option -contat, but if try get the acf of the interaction the program always has a crash, I also

[gmx-users] purpose of step pdb files during MD

hi guys, from time to time i'm faced with GMX output files during MD called, e.g. in the current case: step8164372b_n254.pdb step8164372b_n2.pdb step8164372c_n254.pdb step8164372c_n2.pdb what i know is that they are related to kind of exploding systems. however, i'm not really able to

Re: [gmx-users] gromacs ligand topology file for "GNP"

On 9/6/17 3:46 PM, Deep kumar wrote: Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong. a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule

[gmx-users] gromacs ligand topology file for "GNP"

Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong. a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule type. b) Entered the "net charge" by

Re: [gmx-users] Gromacs error: equilibration phase

Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong. a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule type. b) Entered the "net charge" by

Re: [gmx-users] Ionic liquid simulation problem

Hi Ghosh, Thanks for your answer. But I'm not sure if I understood what you meant. I already used insert-molecules command to create a box with the cationic species. Now, should I use the same command to include the anionic species into the box? Best *Prof. Dr. Ednilsom OrestesDepartamento de

[gmx-users] Modeling of the shear flow of the liquid using DEFORM

Dear GROMACS users, I would like to perform non-equilibrium simulation adding a shear flow on the liquid in my bio-membrane system composed of lipids and water. By means of the applications of the deformations I would like to shear a water in X-Y dimensions along the surface of the membrane.

Re: [gmx-users] successive removal of position restrain?

On 9/6/17 5:36 AM, Seera Suryanarayana wrote: Dear gromacs users, I have gone through one gromacs tutorial of md simulation in solvent. Where they mentioned that successive removal of position restrain. In other words first they have done NPT ensemble with 1000 1000 1000 energy constants,

Re: [gmx-users] successive removal of position restrain?

On Wed, Sep 6, 2017 at 5:36 AM, Seera Suryanarayana wrote: > Dear gromacs users, > > I have gone through one gromacs tutorial of md simulation in solvent. Where > they mentioned that successive removal of position restrain. In other words > first they have done NPT ensemble

Re: [gmx-users] GPU-accelerated performance

On Wed, Sep 6, 2017 at 4:58 AM, Alex wrote: > Hi all, > > We just got the new machines that were actually built with Szilárd's > advice (a while back) and I am doing some preliminary tests. "My" machine > has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan

[gmx-users] HPC performance in Gromacs ?

Thanks, Pall, I thought more threads will make the simulation faster. Is it not the case for Gromacs? I have tried to change the values. The file is provided here, https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYeko4d1VwUURCb00/view?usp=sharing . The command line is "gmx_mpi_d mdrun -s

Re: [gmx-users] GPU-accelerated performance

First, take my wow!!! thats a huge system. I would try the combinations of ntmpi XX and ntomp XXX for better performance. Currently with 3 x GPU 1070 for ~11 K system im getting around 50 ns/day (12 core processor). So I guess you can fly here. :) -- Gromacs Users mailing list * Please

Re: [gmx-users] Error while running perl distances.pl

Well to better understand what is going on I suggest:* use strict; line tells to search for possible problems even if script can go on like it is.Maybe just remove it? * remove &>/dev/null or even better use other file instead of /dev/null like dump.txt You will see it that system call is all

[gmx-users] successive removal of position restrain?

Dear gromacs users, I have gone through one gromacs tutorial of md simulation in solvent. Where they mentioned that successive removal of position restrain. In other words first they have done NPT ensemble with 1000 1000 1000 energy constants, then re executed the NPT ensemble with 100 100

[gmx-users] GPU-accelerated performance

Hi all, We just got the new machines that were actually built with Szilárd's advice (a while back) and I am doing some preliminary tests. "My" machine has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan Xp GPUs. So far, I got good test system performance (~11K atoms, 92

Re: [gmx-users] Error while running perl distances.pl

Hello Vytautas, I changed the script file to gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\' rest is same but it showed the same error as previous one. Error readline() on closed