My understanding is that the v-site algorithm is used for the virtual sites and LINCS is used for bonds not involving v-sites (and also angles if you choose contraint=angles).
On Sat, Jun 18, 2011 at 4:40 PM, [email protected] < [email protected]> wrote: > Thank you Roland. > > I did use: > > constraints = all-bonds > lincs-iter = 1 > lincs-order = 6 > constraint_algorithm = lincs > > From looking at the manual, I figured that angle and bond constraints > would all be done by LINCS if I had done (A): > > pdb2gmx -vsite none > constraints = h-angles > (a combination that I have never tried) > > But when I use (B): > > pdb2gmx -vsite hydrogen > constraints = all-bonds > > It seems possible to me that LINCS is not used but instead the > position of the atom is simply built from a mathematical function. > Perhaps this all stems from my lack of thorough understanding of > LINCS, but it seems to me that there need be no iteration to simply > place an atoms based on virtual_sites3 (which are constructed by > pdb2gms -hydrogen) > > For now, I'll simply add a line to state that I built virtual sites > for hydrogen atoms to make it clear, but I'd still like to understand > the difference between options A and B, above, if you have some time. > > Thank you again, > Chris. > > > > > > On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca < > chris.neale at 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 [email protected] > 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 [email protected]. > 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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