[gmx-users] Saving trajectories of a particular group within the system

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 23 20:07:03 CET 2008

Hi Jeroen, Wade

I missed that one.., also in the source (haven't checked where it is
in that case). But it seems you're right, and the original post then
leavves me blue.


Check the .mdp file that is generated by grompp, and see what it says
for xtc-grps. Please report back to the list.



On Tue, Dec 23, 2008 at 1:42 PM, van Bemmelen
<J.J.M.vanBemmelen at student.tudelft.nl> wrote:
> Hi Tsjerk,
> So the claim in the online manual (under
> http://www.gromacs.org/documentation/reference_3.3/online/mdp_opt.html#g
> eneral), that "the difference between a dash and an underscore is
> ignored", is incorrect according to you? Or is it only incorrect for the
> option "xtc-groups"?
> If incorrect I'd say this should be changed asap. But actually I believe
> it is correct, at least for the options I've tried.
> Thanks,
> Jeroen
>>Date: Tue, 23 Dec 2008 11:53:24 +0100
>>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>>Subject: Re: [gmx-users] Saving trajectories of a particular group
>>       within the      system
>>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>>       <8ff898150812230253q3e1c4267te672a59a44948d0a at mail.gmail.com>
>>Content-Type: text/plain; charset=ISO-8859-1
>>Hi Wade,
>>> I intend to generate only the trajectories of my protein alone,
>>> without outputing trajectories of the solvents. This is since the
>>> output files can get really massive. So looking at the manual, I've
>>> inserted the line: "xtc_grps = Proteins" into the .mdp input
>>file and
>>> did a short simulation to try it out.
>>"Proteins" is not a standard group, but from the paste of your
>>.mdp file it seems you used "Protein" instead, which is
>>correct. Please try to stick to literal representations.
>>The real problem seems to be that "xtc_grps" is not correct,
>>but should be replaced with "xtc-grps". This almost brought me
>>to shouting "RTFM",  but a quick glance showed that the manual
>>disagrees with the source code at this point (both for 3.3.1
>>and 4.0.2). So, not your fault, really, but the correct line
>>should read
>>xtc-grps = Protein
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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