Maybe I'm confused here, but the manual says that the pull code will not in general work for groups that have other constraints.
To quote the last part of section 6.3: There is one important limitation: strictly speaking, constraint forces can only be calculated between groups that are not connected by constraints to the rest of the system. If a group contains part of a molecule of which the bondlengths are constrained, the pull constraint and LINCS or SHAKE bond constraint algorithms should be iterated simultaneously. This is not done in GROMACS. This means that for simulations with constraints = all-bonds in the .mdp file pulling is, strictly speaking, limited to whole molecules or groups of molecules. In some cases this limitation can be avoided by using the free energy code, see sec. 6.4. In practice the errors caused by not iterating the two constraint algorithms can be negligble when the pull group consists of a large amount of atoms and/or the the pull force is small. In such cases the constraint correction displacement of the pull group is small compared to the bond lengths. So it sounds like you might be OK if you use a small pull force. The free energy code is also problematic for measuring the forces because it creates a cycle of constraints, which yields an occasional but problematic spike to huge values when trying to calculate the free energy as a function of end-to-end distance of a peptide. Warren Gallin On 2010-10-19, at 6:50 AM, chris.ne...@utoronto.ca wrote: > yes. use the pull code. check your convergence carefully. > > --original message -- > > Hi All, > > I was wondering if it is possible to pull on a single chain? I would like to > anchor the C-terminus and pull the N-terminus and have a plot of pulling > force vs displacement. > > I'm looking for more or less a yes or no answer, if you would like to > elaborate then I won't complain :) > > Thanks, > Joe > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/625c900f/attachment.html > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface or > send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
