[gmx-users] Try NVIDIA's GPU-Ready Applications Installation, Running, Benchmark "Recipe" for a quick on ramp to GROMACS on GPUs

As everyone on this list knows, GROMACS is a versatile classical molecular dynamics application that simulates Newtonian equations of motion for systems with up to millions of particles. Now, you can take advantage of GPUs to get incredibly fast results when running your molecular dynamics

[gmx-users] Ligand topology

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs users Is there any way to create ligand topology file by using pdb2gmx instead of prodrg? Because i use gromos

Re: [gmx-users] vdW and Coulombic forces

On 24/07/17 16:25, diana p wrote: Dear gmx users, I calculated the total force exerted on the particle in the simulated system using g_traj command. I want to decompose the total force into various contributions including vdW and Coulombic. Can anyone suggest a method? I would be more than

[gmx-users] vdW and Coulombic forces

Dear gmx users, I calculated the total force exerted on the particle in the simulated system using g_traj command. I want to decompose the total force into various contributions including vdW and Coulombic. Can anyone suggest a method? I would be more than pleased if someone could guid me.

Re: [gmx-users] changing cutoffs with gmx tune_pme

Hi, On Mon, 24 Jul 2017 14:48 Leandro Bortot wrote: > Dear users, > > I'm doing some tests with gmx tune_pme to optimize the setup for my > system. In the help options I saw that I could change the coulomb and LJ > cut-offs in addition to varying the number of PME

[gmx-users] changing cutoffs with gmx tune_pme

Dear users, I'm doing some tests with gmx tune_pme to optimize the setup for my system. In the help options I saw that I could change the coulomb and LJ cut-offs in addition to varying the number of PME ranks. So I did that to test. My system runs faster when rcoulomb and rvdw are

Re: [gmx-users] ForceField for Zn

…here: https://kamerlinlab.com/ On 24 Jul 2017, at 14:14, Erik Marklund > wrote: Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind regards, Erik

Re: [gmx-users] ForceField for Zn

Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

[gmx-users] ForceField for Zn

Hello to all In my pdb structure their are two ion of Zn; Can anyone suggest which forcefield is appropriate for that. With regards Anjali Patel Research Scholar Department of Physics The M S University of Baroda, Vadodara-390002 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Methodology to determine permeability and diffusivity by constrained water molecule using umbrella constraint

Dear users, If a molecule is constrained in Bilayer using COM pulling. And I am interested in recording force. Which will be used for calculating PMF and subsequently diffusivity and permeability. I am using pull = constraint Can I use pull = umbrella? How to get the force and use it to

[gmx-users] PMF ligand membrane protein

Dear Gromacs User, this is the first time I am attempting membrane protein simulation. I wish to obtain a PMF value for a ligand permeating through a membrane protein (lacY permease). In the Xray str. the ligand is almost at the center of the protein. I wish to generate enough initial