On Sat, Jun 18, 2011 at 4:13 PM, chris.ne...@utoronto.ca < chris.ne...@utoronto.ca> wrote:
> Dear Users: > > If I create the topology of a peptide like this: > > pdb2gmx -f protein.gro -vsite hydrogens > > And then simulate it in vacuum, is lincs used at all? I believe that > it is, as if I use a timestep that is too large then I get LINCS > warnings about angles rotating more than 30 degrees, but that warning > message could possibly have been written with the assumption that I > used LINCS and not virtual hydrogens. > Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. > > Finally, is there a method that needs to be named or cited in relation > to the fact that the angles are now constrained? Is that also done > with P-LINCS? > This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland > > Thank you, > Chris. > > > -- > 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 > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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