I would like to run QM/MM MD where only *part* of the QM region (waters in
TIP3P geometry) is constrained by SHAKE. That is, there are several C-H
bonds which I would like to leave unconstrained if I can help it. The
reason being, and perhaps people have opinions on this as well, that I would
like to compare to other simulations with no QM waters in which I did not
use SHAKE.
My understanding from the manual is that qmshake is all or none wrt bonds
with hydrogen. I can think of two doable, but arguably outlandish, ways to
accomplish this. Will either of these work? Is there a better way to do
this?
1.) Manually go into the parm7 and change the BONDS_INC_HYDROGEN and
BONDS_WITHOUT_HYDROGEN tables... yuck! and will probably fail at first
2.) Create a new atom type for hydrogens bound to carbons (maybe I can steal
one of the halide symbols?) so that leap does not recognize them as bonds
with hydrogen. Of course this new atom type would have the same mass as
hydrogen. Is that enough to trick leap?
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Jul 26 2011 - 09:00:02 PDT
