Hi Brian et al,
> 1) To make a single molecule from 2 things that are not, I think the
> easiest
> thing to do is use the "bond" command in leap and make a new prmtop.
> I'd
> have to look it up in the manual to tell you exactly how to use it.
> Leap
> may complain if any resulting bond, angle, or dihedral terms are not
> defined
> in your parm.dat file (hence the need for an additional frcmod). Keep
> in
> mind also that this might also affect 1-4 scaling of electrostatics,
> but I
> would assume that your QM region is large enough that this is not a
> problem.
You should really NOT need to mess with any of this. The QM code knows about
periodic boundaries and should image things correctly. What happens
internally in the code is that the first QM atom is moved to the origin and
then everything is imaged around this giving you a QM region within the
central box. Then the atoms that are within the cutoff are included and this
makes essentially an imaged QM region with a qmcut buffer of MM atoms around
it and this is what is used in the direct space part of the QM calculation.
If you are having to mess with putting QM residues in the same molecule etc
then there is something very wrong with your QM region.
I suspect you are trying to run a QM region where the residues you are
including are a long way away from each other or drift apart from each other
during the simulation. The QM cut, for stability within the SCF calculation
is a different to the traditional MM cutoff. Here ANY MM atom that is within
QM cut of ANY QM atom is included in the list for ALL QM atoms. This means
you essentially have a surface layer of thickness qmcut surrounding your QM
region. Thus if you have two QM regions a long way apart you will get a
bunch of MM atoms on one side of your box included in the direct space part
of the QM region on the other side. When the code checks for the minimum
image convention you run into problems because your QM-MM region is huge and
overlaps the box edges.
The code is simply not designed at present to deal with this situation.
There are two approaches
1) Code in support for multiple QM regions. This needs careful thinking
about to be able to do it in a formerly correct way, conserving energy etc.
2) Use an adaptive QMMM method to transform one of your QM molecules into MM
when it diffuses away from the other or a given location.
The second one is work in progress, the 1st is on the wish list.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Thu Oct 06 2011 - 09:30:02 PDT
