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

[chris.neale at utoronto.ca]

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.

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?

Thank you,
Chris.