[gmx-users] question on merging trajectories files

Dear GROMACS users, which script should I use in GROMACS to unite several trajectory files? Like in ptraj in Amber I can merge dierent .mdcrd iles. Can I use one of those scripts for this: http://manual.gromacs.org/current/online/trjconv.html http://manual.gromacs.org/current/online/trjcat.html

[gmx-users] question about GROMACS installation on cluster

You will need an up to date version of MPI or PVM. Set USE_MPI or USE_PVM to yes in your Makefile.$GMXCPU and type: cd $GMXHOME/src in which file should i type this? I can find makefile.in and makefile.am in the distribution directory where I unpack GROMACs and in the src directory. Which of th

[gmx-users] amber ports folder in GROMACS

Dear GROMACS users, I m trying to port amber force fields to my GROMACS in my local folder on cluster. as is written here http://chemistry.csulb.edu/ffamber/ "(5)Files for each force field are located in a seperate subdirectory, such as ffamber94/ for the Cornell potential. Copy the desired f

[gmx-users] (Без темы)

Dear GROMACS users, we want to make a refinement of protein structure by distributed computing MD calculations. For this we need to make random initial coordinates generation for 100 of 100 ps trajectories. It is something like fold...@home strategy uses for folding, but we want to get the traje

[gmx-users] file conversion from Amber to GROMACS for protein-ligand complexes

? 2. Make .gro and .top files for ligand and protein separately and then to combine them to one .gro file and one .top file for protein-ligand complex simulation if it is possible. Best regards, Andrew Voronkov ___ gmx-users mailing listgmx-users

[gmx-users] Small molecule-protein complexes MD simulations

This is of course the question which was discussed many times, but I just want to ask about updates for it. Is there any port for GAFF force field now? Is it possible to prepare small molecule ligands for GROMACs MD with Amber force fields without Amber version installed? Best regards, Andrew

[gmx-users] is there a possibility to convert .gro files directly to PDB?

Dear GROMACS users, is there a possibility to convert .gro files directly to PDB? Or I can do it only with .tpr? I've tried gro2pdb -f conf.gro -o conf.pdb but it doesn't work. Best regards, Andrew ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Isn't dt=0.0001 very small?

Dear GROMACS users, I'm doing this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during equilibration. It works only with dt=0.0001 which seems very very small step for me. Is it ok or I need to clean up

[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58

> Message: 3 > Date: Fri, 06 Mar 2009 13:41:28 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] .gro files problems > To: Discussion list for GROMACS users > Message-ID: <49b16e58.3000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=f

[gmx-users] .gro files problems

Dear GROMACS users, I'm trying to do this tutorial with 1ijy structure from rcsb.org All .gro files on different step raise questions. 1) conf.gro - by VMD I see some strange groups which are not linked with the protein. 2) After solvatation step in solvated.gro the protein is not in the middle o