On 19/06/2011 6:13 AM, chris.ne...@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.
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