Hey
you are right, what you want to do is not doable through the qm/mm
interface as is. qm shake will do ALL heavy-H bonds in the qm region, no
choice for the user.
Option 1 is 'doable' but yu can get in tons of trouble !
Option 2 seems like a lot of work.
let me suggest option 3. Add a strong distance restraint between the
atom that you want 'shaken'. You need to play a bit with this, because a
too-large force constant will destroy the integrator, and one too soft
will do nothing useful.
Adrian
On 7/26/11 5:57 PM, Brian Radak wrote:
> 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
>
>
--
Dr. Adrian E. Roitberg
Full Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Tue Jul 26 2011 - 09:30:03 PDT
