[gmx-users] Re: Remove solvent from results

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 10 19:07:57 CET 2009

Jack Shultz wrote:
> I guess it can be done with sed but is there another way using one of
> the Gromacs apps?

Use trjconv, with a special index group that defines all non-solvent atoms (or 
whatever subset you want to save).  You can also do this ahead of time by 
setting the appropriate xtc_grps in the .mdp file.


> On Tue, Nov 10, 2009 at 12:48 PM, Jack Shultz
> <js at drugdiscoveryathome.com> wrote:
>> Hi Guys,
>> I was wondering if there is any way to remove the solvent from your
>> final trajectory results in mdrun?
>> --
>> Jack
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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