[gmx-users] grompp error(Segmentation fault)in gromacs version 5.0.6

Hi,    I carry on md run on protein-dna complex using  AMBER99SB-ILDN force field. Here I state my problem.   gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top -water tip3p -ignh  it compile successfully.  gmx_mpi editconf -f em267_processed.gro -o em267_newbox.

[gmx-users] Regarding Dynamic cross correlation map analysis

VMD tutorial on Dynamical Network Analysis .Here psf and dcd files have been used to create the network.My question is :Is it possible to do Dynamical Network Analysis using VMD through GROMACS trajectories?With Regards,Soumi Das -- Gromacs Users mailing list * Please search the archive at

[gmx-users] MDsimulation of Protein-DNA complex

he  carbon atom of the carboxyl group of the negatively charged Asp 129 residue.How can the positions of Na+ ions around DNA be constrained within 5 A from the PO4- groups of DNA backbone by which command or method using  gromacs exclusively (not AMBER TOOL /AMBER PACKAGE )?With Regards ,Soumi Das -

[gmx-users] Fw: MDsimulation of Protein-DNA complex

From: "soumi "<soum...@rediffmail.com>Sent: Tue, 03 May 2016 19:24:22To: <gromacs.org_gmx-users@maillist.sys.kth.se>Subject: Fw: MDsimulation of Protein-DNA complexFrom: "soumi "<soum...@rediffmail.com>Sent: Tue, 03 May 2016 19:21:47To: <gmx-us...@gro

[gmx-users] Fw: MDsimulation of Protein-DNA complex

From: "soumi "<soum...@rediffmail.com>Sent: Tue, 03 May 2016 19:21:47To: <gmx-us...@gromacs.org>Subject: MDsimulation of Protein-DNA complexDear All, I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order

[gmx-users] Problem using gromacs

Respected Sir, I am new user of gromacs. When I use the following command gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr I get the following error :Number of coordinates in coordinate file does not match topology file. Please tell me how can I correct the number o