[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.gro -c -d 1.0 -bt

[gmx-users] Regarding Dynamic cross correlation map analysis

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

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

From: soumi soum...@rediffmail.comSent: Tue, 03 May 2016 19:24:22To: gromacs.org_gmx-users@maillist.sys.kth.seSubject: Fw: MDsimulation of Protein-DNA complexFrom: soumi soum...@rediffmail.comSent: Tue, 03 May 2016 19:21:47To: gmx-us...@gromacs.orgSubject: MDsimulation of Protein-DNA

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

From: soumi soum...@rediffmail.comSent: Tue, 03 May 2016 19:21:47To: gmx-us...@gromacs.orgSubject: MDsimulation of Protein-DNA complexDear All, I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order to neutralize the net charge

[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