I am sorry I did not express myself clearly.
Let us say, the coordinate of A is (1,0,0) and the coordinate of B is (2,0,0). So B is on the right side of A.
The finally result I want is Distance(AB) is 5 but B has to be on the left side of A, such as: B (-4, 0, 0) and A (1, 0, 0)
Like you said, umbrella sampling cannot do this.
So what should I do? Is steered MD can set the pulling direction? If it can, how can I do it? Thanks.
Sincerely,
Qian
----- Original Message -----
From: Brian Radak <radak004.umn.edu>
Date: Saturday, January 28, 2012 4:24 pm
Subject: Re: [AMBER] Can I set the direction of the pulling force?
To: AMBER Mailing List <amber.ambermd.org>
> 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
> > _______________________________________________
> > 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
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Received on Sat Jan 28 2012 - 15:00:02 PST
