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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