Hi, Things change between versions when we recognize limitations of old decisions. 5.0 certainly recognizes pull-ngroups, so I think you were using a non-matching grompp at some point. You do have the option of reading the .mdp documentation for the version you're using. :-) (Of course, if it's out of date, let us know and we'll fix it!)
Mark On Mon, Oct 5, 2015 at 9:10 AM Kutzner, Carsten <ckut...@gwdg.de> wrote: > Hi, > > take a look at the mdout.mdp grompp output file. There you should see > how the pull-related parameters are called in the version you were using. > Maybe you just need to use minus signs instead of the underlines. > > Best, > Carsten > > > > On 05 Oct 2015, at 04:25, Stella Nickerson <stella.nicker...@gmail.com> > wrote: > > > > I am attempting to pull a particle across a simulation box. I did it > > several times with version 4.6.3 but this is my first attempting to do it > > with version 5.0.4. > > > > I modified my mdp file for the new version based on the updated tutorial > ( > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html > ). > > My pull code looks like this: > > > > ; Pull code > > pull = yes > > pull_ngroups = 2 > > pull_ncoords = 1 > > pull_group1_name = DMY > > pull_group2_name = DNP > > pull_coord1_type = umbrella > > pull_coord1_geometry = direction_periodic > > pull_coord1_groups = 1 2 > > pull_coord1_dim = N N Y > > pull_coord1_rate = 0.01 > > pull_coord1_k = 1000 > > pull_start = yes > > > > I am getting an error message and several warnings. The error reads > > "Invalid enum 'yes' for variable pull, using 'no' Next time use one of: > > 'no' 'umbrella' 'constraint 'constant force.' > > > > The warnings read "unknown left-hand 'pull_ngroups' in parameter file", > > with similar warnings for the other left-hand terms. > > > > I tried to compile a version using my old pull code from the earlier > > version just to see what would happen and it gave fewer warnings, though > it > > didn't recognize "pull_vec1." So neither the old options nor the new > > options work. > > > > I would love some clarification on this issue. > > > > Thanks, > > > > Stella Nickerson > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.