[gmx-users] Automatically assign the protonation states for pdb2gmx

I want to run more than 300 MD, each with a different PDB (more precisely, variants derived from a same wild type). I need to manually assign the protonation states using the "-inter" option every time, which is impossible for more than 300 times. gmx pdb2gmx -f protein.pdb -o

Re: [gmx-users] How to avoid the infinite potential energy in simulations of dimers?

Dear Justin Lemkul, Thanks for your reply. I just downloaded the Cryo-EM structure of the dimer from RCSB, added missing residues using Modeller and built systems by the following commands: gmx pdb2gmx -f dimer.pdb -o dimer.gro -p dimer.top -water tip3p -ff amber99sb-ildn -ignh

Re: [gmx-users] REMD stall out

This was not actually the solution. Wanted to follow up in case someone else is experiencing this problem. We are reinstalling the openmp version. On Thu, Feb 20, 2020 at 3:10 PM Daniel Burns wrote: > Hi again, > > It seems including our openmp module was responsible for the issue the > whole

Re: [gmx-users] How to avoid the infinite potential energy in simulations of dimers?

On 2/21/20 5:11 AM, Qing Liu wrote: Dear Gromacs users, I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: Step 2029: The total potential energy is nan,

[gmx-users] Regarding gpu acceleration

Dear sir, I am trying to use gpu for gromacs. It gives error as "cuda is depracted". I am using Ubuntu 18.04.4 Cudua toolkit 10.2 Gromacs 2018.1 gcc version 7.4 Nvidia driver version 435 Nvidia GTX GeForce 1050 Ti Does these Versions support gpu acceleration? Plz help. -- Gromacs Users mailing

[gmx-users] How to avoid the infinite potential energy in simulations of dimers?

Dear Gromacs users, I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: Step 2029: The total potential energy is nan, which is not finite. The LJ and

[gmx-users] Thesis developed software; which Open-source License?

Greetings comrades. This question may be somewhat redundant, so dont expect reply to every aspect, may ask at RG also. However if anyone have more or less insight, please reply. My thesis has calculation software that are built upon partly innovative and partly basic calculation/plotting/graphing

Re: [gmx-users] Regarding to pme on gpu

Hi. On Tue, Feb 18, 2020 at 5:11 PM Jimmy Chen wrote: > > 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? This is a limitation of the implementation,