AMBER Archive (2009)

Subject: Re: [AMBER] Partial interactions

From: steinbrt_at_rci.rutgers.edu
Date: Mon Apr 20 2009 - 16:47:35 CDT

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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>

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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