Ah ok, so the relative position at the start is incorrect? I would think
the simplest way to fix that is to just rebuild the system in that
configuration. If you are using periodic boundary conditions you can try
to exploit them, but restraints in AMBER are applied to the minimum image
and I don't exactly know what would happen if the identity of that image
changes (I'm not even sure what I would want expected behavior to be in
this case).
Is the path of this transition what is of interest? I'm not hugely
familiar with all of the steered and targeted MD modules in AMBER, but I
think that is what you would want in that case. There is extensive
documentation in the manual on those.
Brian
On Sat, Jan 28, 2012 at 5:37 PM, Qian Wang <qwang.mail.uh.edu> wrote:
> 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
> > > _______________________________________________
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> > > 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 :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> > appropriateaddress.
> > _______________________________________________
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> _______________________________________________
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>
--
================================ 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 - 15:00:03 PST
