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

[Roland Schulz]

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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