[gmx-users] Fwd: Query regarding Preferential Interaction Coefficient Calculation

Dear all, I want to calculate the number of water and osmolyte molecule at particular distance from surface of protein in order to calculate preferential interaction coefficient. I had calculated it using gmx select command. Is it right to calculate using this command. Please help me in this

Re: [gmx-users] gmx 2019 performance issues

On Tue, Jan 15, 2019 at 1:30 PM Tamas Hegedus wrote: > Hi, > > I do not really see an increased performance with gmx 2019 using -bonded > gpu. I do not see what I miss or misunderstand. > The only thing I see that all cpu run at ~100% with gmx2018, while some > of the cpus run only at ~60% with

Re: [gmx-users] different nvidia-smi/gmx GPU_IDs

Szilard, Is the environmental variable set at build ? thanks Paul > On Jan 18, 2019, at 12:36 PM, Szilárd Páll wrote: > > Hi, > > The CUDA runtime tries (and AFAIK has always tried) to be smart about > device order which is what GROMACS will see in its detection. The > nvidia-smi monitoring

Re: [gmx-users] different nvidia-smi/gmx GPU_IDs

Hi, The CUDA runtime tries (and AFAIK has always tried) to be smart about device order which is what GROMACS will see in its detection. The nvidia-smi monitoring tools however uses a different mechanism for enumeration that will always respect the PCI identifier of the devices (~ the order of

[gmx-users] RMSD plots protein-protein complex

Hello I did a simulation of protein-protein interaction with Gromacs code. In this simulation, the number of amino acids in each protein is about 230. The simulation production run was 300ns. After analyzing trajectory, I found that RMSD value of protein-protein complex fluctuated near 1.8 nm but

Re: [gmx-users] perl water_deletor.pl

Hi On Fri, Jan 18, 2019 at 3:30 AM rabee khorram wrote: > *Hello everyone, * > *I am running liposome structure with gromacs 5.* > *this liposome created with Packmol software(without water molecules).* > *after Solvating liposome with water in gromacs, I need to remove waters > from hydrophobic

[gmx-users] Problem in velocity plot while doing MD simulation of DNA protein with E field

Hi, I am trying to study the motion of protein along a DNA with application of electric field. I have position restrained the DNA, and the DNA axis is along Z, and I am applying an electric field also along +Z. Now since the protein is strongly positively charged it moves along the DNA in the

Re: [gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

Thank you so much, Justin and Mark! -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 18, 2019 09:55 PM To: "gromacs.org_gmx-users"; Subject: How the "Fmax" is determined without "emtol" in the mdp file? I am doing an energy

Re: [gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

Hi, There are defaults, and documented online: e.g. http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#energy-minimization Mark On Fri, Jan 18, 2019 at 2:56 PM ZHANG Cheng <272699...@qq.com> wrote: > I am doing an energy minimization in a vacuum condition. There is no

Re: [gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

On 1/18/19 8:55 AM, ZHANG Cheng wrote: I am doing an energy minimization in a vacuum condition. There is no "emtol" in the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown below. So how this "< 10" is determined? Every keyword that requires a numerical setting

[gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

I am doing an energy minimization in a vacuum condition. There is no "emtol" in the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown below. So how this "< 10" is determined? Steepest Descents converged to Fmax < 10 in 4063 steps Potential Energy = -2.3973977e+04

Re: [gmx-users] perl water_deletor.pl

Hi, I think you can write your script to delete it by defining the center of liposome and searching for water molecules in a range of hydrophobic radius from that center I suggest awk scripting language Best, Quyen On Fri, Jan 18, 2019 at 9:30 AM rabee khorram wrote: > *Hello everyone, * > *I

[gmx-users] How to visualise the dodecahedron in Pymol or VMD?

I use gmx editconf -f protein.pdb -d 5 -bt dodecahedron -o protein.gro to put the protein in a dodecahedron. However, when I open the protein.gro in pymol, and type "show cell", only a triclinic box is shown. So how to visualise the dodecahedron in Pymol or VMD? -- Gromacs Users mailing

[gmx-users] perl water_deletor.pl

*Hello everyone, * *I am running liposome structure with gromacs 5.* *this liposome created with Packmol software(without water molecules).* *after Solvating liposome with water in gromacs, I need to remove waters from hydrophobic region.* *is these any "perl water_deletor.pl