[gmx-users] To invoke GPU in gromacs version 4.6.4

i am trying to invoke GPU for my final mdrun step using the command mdrun -v -deffnm md -gup_id Got the following : GPU ID string set, but mdrun was compiled without GPU support. I have also included cutoff-scheme = Verlet in the md.mdp file. Kindly help me to troubleshoot this

Re: [gmx-users] 100-quartz force field for GROMACS using CGenFF

Dear Justin, thank you for your prompt answer. I will contact you off-list. Best Ivan On 2017-03-05 17:14, Justin Lemkul wrote: On 3/5/17 6:56 AM, Ivan Gladich wrote: Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force

Re: [gmx-users] NPT equilibration without pbc

Thanks Alex for the suggestion!! On 5 March 2017 at 01:49, Alex wrote: > I looked at that paper and there are no attempts to simulate liquid-gas > equilibrium at normal atmospheric pressure. That aside, what the authors > did instead is actually pretty mind-boggling: they

Re: [gmx-users] 100-quartz force field for GROMACS using CGenFF

On 3/5/17 6:56 AM, Ivan Gladich wrote: Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental

Re: [gmx-users] membrane proteins simulation

On 3/5/17 1:44 AM, Negar Parvizi wrote: Dear all users, I am new in membrane proteins simulation. I want to simulate a membrane protein that it is a part of a large protein and has a big extracellular part.Here is my question: is it ok, I just simulate the membrane part even it is a part

Re: [gmx-users] UMBRELLA SAMPLING

On 3/4/17 9:24 AM, Subashini .K wrote: Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website,

[gmx-users] 100-quartz force field for GROMACS using CGenFF

Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental material of Lopes, P.E.M., Murashov,

Re: [gmx-users] NPT equilibration without pbc

I looked at that paper and there are no attempts to simulate liquid-gas equilibrium at normal atmospheric pressure. That aside, what the authors did instead is actually pretty mind-boggling: they replaced the droplet with a cylinder by making the system periodic in the out-of-plane direction.