>>
>> 4) What is the time scale for a reaction to happen ( is it in atosec or
>> femtosec time scale?) ?
>See item 2) above. Proton transfer reactions are usually on the
microsecond
>or slower time scale, and you will essentially never see them happen
>spontaneously in an MD simulation.
>From my experience (I've run quite a bit of QM/MM) and what I've observed
in the literature it *is sometimes possible to see spontaneous reactions*,
however, these are often orthogonal to the direction you expected the
system to progress. I've actually experienced/seen this reported for proton
transfer reactions a few times. In my opinion this is very suspcious and
most probably a result of unphysical forces (*e.g. *large restraints), bad
starting conditions (*e.g.* bad atom overlaps), or a chemically unrealistic
Hamiltonian (*e.g.* geometry disagreement with MM and semiempirical
methods). I would actually be very worried if I saw a spontaneous reaction
and would certainly think long and hard before reporting it in the
literature (although this doesn't seem to stop a large number of JACS
papers). The most convincing support I can think of is in fact including
such a process in the reaction coordinate (easier said than done!)
utilizing any of the techniques already mentioned.
Regards,
Brian
On Wed, Jun 18, 2014 at 8:54 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Wed, Jun 18, 2014, Tanmoy Paul wrote:
> >
> > 1) How the program recognize the atoms which are supposed to take part in
> > the reaction ( because there are lots of other atoms in the qm -zone) ?
>
> Amber doesn't know that any reaction is "supposed" to take place. In the
> setup you describe, that would have to take place spontaneously.
>
> >
> > 2) Is there any average time limit for any reaction to occur ( like in my
> > case the proton transfer ) because it will give me some idea about how
> long
> > I have to continue ?
>
> This depends *very* strongly on the type of reaction you are studying. If
> you
> can estimate the reaction barrier, you could use transition state theory to
> get a rough estimate of the time scale.
>
> >
> > 3) Can I see the reaction happening in VMD ?
>
> Yes.
>
> >
> > 4) What is the time scale for a reaction to happen ( is it in atosec or
> > femtosec time scale?) ?
>
> See item 2) above. Proton transfer reactions are usually on the
> microsecond
> or slower time scale, and you will essentially never see them happen
> spontaneously in an MD simulation.
>
> >
> > 5) Can I do something more meaningful than just waiting for this reaction
> > to happen ?
>
> Yes. Things like umbrella sampling along the reaction coordinate are
> usually
> required. I'd recommend finding a research paper that describes a reaction
> similar to the one you are interested in, and seeing what sorts of
> approaches
> were used. Amber's tutorial A10 walks you through one approach to a proton
> transfer reaction.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ 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 : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
====================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 18 2014 - 07:30:03 PDT
