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.
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