Re: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation

HI However, since I want to pull the protein for a long distance, I should > gradually change the equilibrium length, and I have no idea how to > dynamically change the "pull-coord1-init" during SMD simulation. Or do I > have to restart the simulation with a new .mdp file with different > "pull-c

Re: [gmx-users] Increase Graphene sheet size

Hi On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal wrote: > Hello All, > > I want to create a graphene sheet with a specific dimensions (10*15*0.284) > nm. > > I created a .gro file as below ( as mentioned in this website > > https://erastova.xyz/teaching/practical-simulations-for-molecules-an

Re: [gmx-users] Is Gromos force fields not recommended?

If the GROMOS force-field would clearly not be compatible with GROMACS, we would have removed it from the GROMACS distribution. There are two issues here, which both stem from the fact that the GROMOS force-field has been parametrized with a simulation setup that, for good reasons, can not be re

Re: [gmx-users] Is Gromos force fields not recommended?

This is the warning from Grompp. The GROMOS force fields have been parameterized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the

[gmx-users] Unexpected cudaStreamQuery failure: unspecified launch failure

Hi, I had this error while I was performing a short (1 ns) simulation. It seems to be related to the Nvidia driver. Can anyone please help me understand why I'm having this error? My system is a Ubuntu 18.04.4 LTS with cuda-toolkit version 9.1.85, nvidia driver version 410.78. I had this error:

Re: [gmx-users] Tabulated potentials

So I am using Iterative Boltzmann Inversion to get the CG potentials for a cellobiose-water solution. During the first step of the simulation by gromacs, I get the error, which I think it might be due to some large forces, causing the distance between the CG beads to increase to values more than

Re: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU

Hi Oliver, Does this affect an installation of GROMACS? In previous reports we have observed that the issue is only present when running "make check" in the build tree, but not in the case of an installed version. Cheers, -- Szilárd On Mon, Feb 17, 2020 at 7:58 PM Oliver Dutton wrote: > Hello

[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi

[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delh

Re: [gmx-users] Listing residues in gromacs

Hi Subhomoi, Yes, gmx select can do that (see http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) For what you want to do, it's beneficial to have a look at the selection syntax here http://man

Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

Thank you Alessandra, They are indeed averaged over the simulation time, but the SR values should be zero for these specific pairs of interactions. I managed to "hack" it by defining a bond between them with a force constant of zero. It works! Best, Rosa Op 17-02-20 10:15 heeft gromacs.org_gm

[gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride system, however I’m not entirely sure that I’m setting up the equilibration parameters in the mdp file correctly as I’m getting different simulation result

[gmx-users] CGENFF validation / optimization

Dear all, While suing CGENFF server for " *.str " file generation, Few of the penalties were found to be higher than 50. How to do validation/optimization.? Is there any recommended softwares / servers available for * " extensive validation / optimization." or any standard procedure available to

[gmx-users] GPU considerations for GROMACS

Hello, Previously, I have helped building a workstation for my fellow researcher who heavily uses GROMACS for his MD simulations, with the following base specs: -CPU: 8 cores (Xeon E2278G) -RAM: 32GB -GPU: 1x RTX2080Ti With this setup, he managed to shrink down each simulation runtime to, say a

[gmx-users] How to cap a single residue in gromacs

Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I added ACE and NME terminals as below in the gro

[gmx-users] Regarding to pme on gpu

Hi, When set -pme gpu in mdrun, only one rank can be set for pme, -npme 1. What is the reason about only one rank for pme if use gpu to offload. Is it the limitation or somehow? I am interesting in any performance improvement is still doable and any improved plan for gpu kernel of pme and pp. ther

[gmx-users] Annealing

Hi all, Using the last frame of a 300ns simulated at 298.1K and it's CPT file I would like to start an annealing simulation, so, I used gmx gromp -t case.cpt and here is a part of output of gromp: Simulated annealing for group Other: Single, 6 timepoints Time (ps) Temperature (K) 00.0 2

[gmx-users] Problem in energy minimization and domain decomposition

Dear Gromacs users I am getting the following message while running an energy minimization:- There is no domain decomposition for 32 ranks that is compatible with the given box and a minimum cell size of 1.85723 nm I am not using any distance restraint, and selecting box size by the following com

[gmx-users] MolVA 2020 Deadline Extension (February 29th) - EuroVis 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

Dear colleagues, We would like to inform you about the extended deadlineforfull papers as well as short papers to: Workshop on Molecular Graphics and Visual Analysis of Molecular Data (co-located with EuroVis & Eurographics

[gmx-users] Regarding to pme on gpu

Hi, When set -pme gpu in mdrun, only one rank can be set for pme, -npme 1. What is the reason about only one rank for pme if use gpu to offload. Is it the limitation or somehow? I am interesting in any performance improvement is still doable and any improved plan for gpu kernel of pme and pp. ther