[gmx-users] is lincs used with virtual hydrogens?

[Roland Schulz]

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, chris.neale at utoronto.ca <
chris.neale at utoronto.ca> 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.
>
>
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