[gmx-users] gmx solvate problem

Hi All, I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the top and below part of the ice surface with solvent (the solvent is tip4p water), some of water molecules go to inside of the ice layers. I did not receive any errors, but the coordinate files became messy after

Re: [gmx-users] DSSP

t; J > > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R <vidyadevi2...@gmail.com> wrote: > > > I got the error > > > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> > /dev/null' > > Reading fra

[gmx-users] BONDS BREAK DURING MINIMIZATION

Hi gromacs users, The bonds of my organic molecule, break while computing rdf. The following sentences appear while first minimization Step 11, time 0.011 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.02, max 0.79 (between atoms 20 and 6) bonds that rotated more

[gmx-users] Unable to write whole trajectory with trjconv and error in gmx check

Dear All, I am facing problem with GROMACS version 2016.1 and 2016.3. I gave a run of 30ns of my protein in our local cluster that uses sbatch to queue the job. My input file for the sbatch is the following: #!/bin/bash #SBATCH -t 5-00:00:00 #SBATCH -N 4 #SBATCH --ntasks-per-node=12

[gmx-users] fixing molar concentrations in gromacs

Hi gmx users, I want to consider one organic molecule of solute dissolved in several molecules of water. How to fix molar concentrations in gromacs ? ( say 0.1 M ) Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

[gmx-users] regarding pbc issue

Hi gmx users, I used the following commands after simulation run (organic compound in water, to calculate rdf) gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx trjconv -pbc mol -center -s PRD.tpr -f

[gmx-users] generating movie file

Hi gromacs users, Can we generate .mp4 file instead of .pdb using gmx trjconv? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] generating movie file

voice as narration to my glorious trajectory, but was > disappointed. Very useful for supplemental files for journals with IF>10. > Maybe gmx developers should look into that. > > > > On 1/26/2018 9:51 PM, Vidya R wrote: > >> Hi gromacs users, >> >> &g

[gmx-users] Question about water insertion

I have one water molecule in my gro file as below: TIP4P 4 1SOL OW1 0.054 0.005 0.022 1SOLHW12 0.009 0.072 0.073 1SOLHW23 0.142 0.041 0.008 1SOL MW4 0.060 0.018 0.026 0.00 0.000 0.000

Re: [gmx-users] regarding pbc issue

-center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc and created a .pdb file with newtraj.xtc, the whole molecule was intact. Thanks, Vidya.R On Sat, Jan 13, 2018 at 7:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/13/18 7:53 AM, Vidya R wrote: > >> Hi

[gmx-users] nano dimensions

Hi gromacs users, How to specify nano dimensions of an organic compound in the input files of gromacs? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] nano dimensions

Thank you for the reply. How to carry out simulations of a molecule in nano scale? Thanks, Vidya.R On Fri, Dec 21, 2018 at 7:11 PM Justin Lemkul wrote: > On Fri, Dec 21, 2018 at 6:35 AM Vidya R wrote: > > > Hi gromacs users, > > > > How to specify nano dimension

Re: [gmx-users] trajectory tools don't work with large .xtc / .trr files

Just one dumb idea. Your ubuntu is 32 or 64 bits? Rafael Rodríguez Pappalardo Depto. Química Física, Univ. de Sevilla El 11/2/2015, a las 13:57, Wojciech Kopeć 9000...@gmail.com escribió: Dear all, I've been using GROMACS successfully for quite some time on several platforms, although

[gmx-users] Walls and PME

Hi, I'd like to simulate a membrane NPT with no pbc in the z direction. I understand I therefore need to use 2 walls. How does the pme work with walls? Is pme 2D only if I introduce wall(s)? Many thanks Sophia Wheeler PhD student Prof J Essex Group University of Southampton -- Gromacs

Re: [gmx-users] How to extend the protein simulation in Gromacs from 1 ns to 150 ns?

As you already run 1ns molecular dynamics now you have md.tpr, md.cpt files in your working directory You need to creat a new tpr file (newmd.tpr) from previous md.tpr file tpbconv -s md.tpr -extend 149000 -o newmd.tpr 149000 is ps then use mdrun -s newmd.tpr -cpi previous.cpt On Thu, Oct

Re: [gmx-users] Fwd: Simulation of surfactant and water composition

Use packmol software for system generation, save it in PDB file and then use appropriate force field . On Thu, Oct 12, 2017 at 8:01 AM, Amali Guruge wrote: > -- Forwarded message -- > From: > Date: Thu, Oct

Re: [gmx-users] phosphorylated protein parametrization

Hi, Which force field you want to use for parameterisation ? On Thu, Dec 7, 2017 at 12:00 PM, wrote: > Hi folks, > what do I need to do to run pdb2gmx with a protein pdb file that contains > phosphorylated THR labeled as THP? I see several solutions but no of

Re: [gmx-users] phosphorylated protein parametrization

https://www.swisssidechain.ch/browse/family/table.php?family=all. Here you can get all the gromaccs topology file for phosphorylated THR ( Charmms FF) On Thu, Dec 7, 2017 at 12:00 PM, wrote: > Hi folks, > what do I need to do to run pdb2gmx with a protein pdb

Re: [gmx-users] itp file for aminoacids

; i dont know what is the problem? > > thanks for your attention > > On Mon, Oct 30, 2017 at 6:25 PM, R C Dash <rcdash0...@gmail.com> wrote: > > > use https://atb.uq.edu.au/index.py / > > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or > > http://swissparam.ch/ >

Re: [gmx-users] itp file for aminoacids

use https://atb.uq.edu.au/index.py / http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or http://swissparam.ch/ or http://vienna-ptm.univie.ac.at/ for .itp file All amino acids are identified bybby AMBER force field. If you there is some modification like methylated lysine you have to creat a

Re: [gmx-users] (no subject)

use trjconv command with nojump option to center all the peptide. Use the starting structure as the starting configuration. regards, RC Dash On Fri, Oct 27, 2017 at 5:51 AM, saranya wrote: > Dear Users, > I have done a simulation of Aggregated amyloid beta peptide for

[gmx-users] Replicating the Results from gmx covar

Hi, I've been developing codes to perform PCA of the alpha-carbons from a processed GROMACS trajectory of a protein in the human-readable .g96 format. I perform the standard post-processing of the trajectory (still in the compressed .xtc version generated from gmx mdrun) as follows: 1) I

[gmx-users] how can I get two parallel lysin in the same box?

Dear all, I am using gromacs 5.1.2 and I am doing simulation with lysin and surfactant. Now in the same box I want two lys30 (two identical lysin) oriented once in parallel and once in orthogonal each other. I tried using gmx insert-molecules ... but it's a random orientation. I also

[gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation

Hi, I've run a fairly long (1 microsecond) trajectory of ubiquitin in spc/e on a supercomputer that allows a 48-hour runtime on their nodes. Since the simulation doesn't finish in 48 hours, I used the checkpoint files from the simulation to restart the simulation, using the following mdrun

Re: [gmx-users] GROMACS Output Timestep Changes Over a Long, Check-pointed Simulation

I'm calculating a time correlation function from the trajectory using an in-house code and I wanted to make sure the timesteps between each frame are the same (i.e. the 0.2 ps write interval specified in the .mdp file). Based on your response, it seems as though they are. Many thanks, Eric

[gmx-users] helping increasing box

Dear all, I am doing COM-pulling simulations between two lysine chains connected with a surfactant. Basically I want to find the force able to separate the two chains. Increasing the force, at some point gromacs was complaining that the distance between the two pull groups is larger that

[gmx-users] how to make index of a micelle

Dear all, In my simulation I have a lysine + micelle of SDS. In the analysis, I want to find the spherical radial distribution functions of methyl groups around the center of mass of the micelle. I Know how to make the index for the methyl group, but how can I make an index for the micelle?

Re: [gmx-users] how to make index of a micelle

Dear Justin, I want to make an index for the micelle, made od 60 molecules of SDS. Thanks for the email. Best, Giuseppe Il 2019-11-18 18:09 Justin Lemkul ha scritto: On 11/18/19 11:43 AM, Giuseppe R Del Sorbo wrote: Dear all, In my simulation I have a lysine + micelle of SDS

Re: [gmx-users] how to make index of a micelle

/19 12:13 PM, Giuseppe R Del Sorbo wrote: Dear Justin, I want to make an index for the micelle, made od 60 molecules of SDS. So, if I understand correctly, the SDS micelle does not contain all of the SDS molecules in the system? That was not clear in your original email. If that's the case

[gmx-users] gmx rdf selrpos seltype

Dear gmx users, I am calculating a spherical radial distribution function between the center of mass of the methyl group of STS (my surfactant) around the center of mass of the STS micelle. I am using this command: gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr -selrpos

[gmx-users] gmx trjconv

Dear users, I might need an help with gmx trjconv. I have a system with a lysine + a micelle attached on it and I have to analyse the radial spherical distribution on the micelle. The idea is to center the micelle and to work on it. I used the command "gmx trjconv - cluster" to get a

[gmx-users] gromacs-error.docx

I've shared an item with you: gromacs-error.docx https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU/view?usp=sharing=59be86ad It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

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