[gmx-users] FWSpider Tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 30 21:51:16 CEST 2010

Hi Nayef,

>> grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr
>> genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log
>> [select Group 12: SOL]
>> pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the
>> file]

This is all fine. You take the structure before em, make a run input
file from it to run genion, adding some ions. You update the topology
file, which seems sensible. But then, mind you that the file with the
ions is fws_ion.gro. That file you should process with the edited
topology to form a run input file for EM. Now look what you're doing

>> mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr &



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list