*******************************************
Vitor Felix
Departments of Chemistry and Health Sciences
University of Aveiro
3810-193 Aveiro
vitor.felix.ua.pt
phone +351 234 370 200 ext: (22102)
http://molecular-modeling.dq.ua.pt
On 26 Jul 2011, at 17:03, Adrian Roitberg wrote:
> 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
