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

[Mark Abraham]

On 19/06/2011 6:13 AM, 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?

Sure - all the backbone bonds, for starters.

> 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.

No, it's real.

> 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?

Yep.

Mark

>
> Thank you,
> Chris.
>
>