Hi Thomas and thanks for your reply. Then I guess I should get into the code
and try to modify it. Is there any document explaining the logic of the
code, what each file does, how the lists of atoms are managed, etc? Or
should I just try brute force?
Regards,
Ignacio
On Mon, Apr 20, 2009 at 5:47 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> you could make molecule A appearing and molecule C disappearing, while B
> stays the same. That way, A and C would never interact. Of course, B would
> only interact with a lambda-dependent, mixed version of the potential from
> A and C.
>
> To get exactly what you describe, I think you would have to modify the
> code, e.g. specifically disregard a given number of interactions.
>
> Kind Regards,
>
> Thomas
>
> On Mon, April 20, 2009 5:07 pm, Ignacio J. General wrote:
> > Dear Amber users:
> >
> > Is it possible to make some molecules of a system interact with only a
> > selected part of the rest, but not with everything else? To be more
> > precise,
> > let's say I have a system with three types of molecules: A, B and C; can
> I
> > do a regular MD but where molecules A only interact with molecules B, not
> > with C (A doesn't see C and viceversa)?
> >
> > Ultimately, I would like to do this in a thermodynamic integration, so
> > that
> > the initial system, V0, is the regular three component system, and the
> > final
> > system, V1, is the unphysical three component system where interactions
> > A-C
> > are not computed.
> >
> > Thanks for your help,
> >
> > Ignacio
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Wed May 20 2009 - 12:07:05 PDT
