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.
Wade, Check the .mdp file that is generated by grompp, and see what it says for xtc-grps. Please report back to the list. Cheers, Tsjerk On Tue, Dec 23, 2008 at 1:42 PM, van Bemmelen <j.j.m.vanbemme...@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" <tsje...@gmail.com> >>Subject: Re: [gmx-users] Saving trajectories of a particular group >> within the system >>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >>Message-ID: >> <8ff898150812230253q3e1c4267te672a59a44948...@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 >> >>Cheers, >> >>Tsjerk > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
