[gmx-users] Residence time

Hi fellow GROMACS users, I have run a 100 ns simulation of a protein in an aqueous solution and I’d like to know if it were possible to calculate the average residence time of water molecules around the protein and/or a specific residue within a given cut-off? Thanks in advance, Can Bora

Re: [gmx-users] simulation on 2 gpus

Stefano, Here is a typical run fpr minimization mdrun -deffnm grofile. -nn gpu and for other runs for a 32 core gmx -deffnm grofile.nvt -nb gpu -pme gpu -ntomp 8 -ntmpi 8 -npme 1 -gputasks -pin on Depending on the molecular system/model -ntomp -4 -ntmpi 16 may

[gmx-users] Perturbation free energy

Dear Justin,I studied your tutorial entitle "Free Energy Calculations: Methane in Water", but I want to know how to calculated free energy based on perturbation theory? I have a drug with a carrier at water medium and I want to calculate free energy but I don't know which kinds of these

[gmx-users] Is it possible to control GPU utilizations when running two simulations in one workstation?

Dear all, I am trying to run a two MD simulations on one workstation equipped with 4 GPU. First I started a simulation with the following command: gmx mdrun -v -deffnm md -ntmpi 12 -gpu_id 0,1 By the nvidia-smi command I find the utilizations of GPU 0 and 1 are 74 and 80%, respectively. Then