I'm not sure I follow your question. Pulling direction, in my mind,
implies a time dependent harmonic potential, like in steered MD. Is that
what you are doing? In umbrella sampling the restraint is usually time
independent and, in some sense, goes both ways as would be necessary for
Newton's 3rd law to hold. Maybe a picture/set of coordinates for your
system before and after would help?
Regards,
Brian
On Sat, Jan 28, 2012 at 1:58 PM, Qian Wang <qwang.mail.uh.edu> wrote:
> Hi,
>
> I am using AMBER10. Assume there are two proteins A and B, orignially the
> distance between the center of mass of A and the center of mass of B is 1 Å
> and A is on the left side of B:
> A B
> what I want to do is to fix the distance to 5 Å, so I applied umbrella
> sampling method. Finally the system became:
> A B
> However, the result I want is:
> B A
> I do not know how to do this. Could anyone help me? Thanks a lot.
>
> Sincerely,
> Qian
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> 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 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Sat Jan 28 2012 - 14:30:02 PST
