[gmx-users] FWSpider Tutorial

[Peicho Petkov]

Hi Nayef,
the next may be useful from technical point of view.
 if you add the option -p with topology file as an argument to given genion 
options you don't have to edit the topology file by hand.
for example
genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log -p 
fws.top -pname NA+

be careful to add the names of both positive and negative ion names cause 
for the given example there will appear 0 NA+ ions in the topology file and 
the names have to correspond to the force field one uses.

Cheers,
Peicho.

----- Original Message ----- 
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
To: <jalemkul at vt.edu>; "Discussion list for GROMACS users" 
<gmx-users at gromacs.org>
Sent: Wednesday, June 30, 2010 10:51 PM
Subject: Re: [gmx-users] FWSpider Tutorial


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
here:

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

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

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