AMBER Archive (2008)

Subject: Re: AMBER: Re: reaction coordinate in umbrella sampling

From: Jerome.GOLEBIOWSKI_at_unice.fr
Date: Tue Sep 23 2008 - 02:33:43 CDT

Hi, I'm not sure there is a simple way to put such restraints. You'll
probably have to put some additional constraints with respect to other
atoms in your system.
But if you intend to compute a PMF from this simulation, be aware that
it will probably be very difficult to unbias your simulation. The
typical 1D-PMF algorithm (used in WHAM for example) is only dedicated to
unbias a single restaint.
Good luck.
Jerome

On Mon, 2008-09-22 at 10:00 -0500, Sudha Mani Karra wrote:
> Hi,
> I am using the Umbrella sampling technique in AMBER 8 to calculate
> the potential of mean force between two molecules. I use the distance
> between their center of masses as the reaction coordinate. Is there
> any way to use the reaction coordinate as the distance in x-direction
> while maintaining their y and z - coordinates unchanged? To be more
> clear, I would like to know if I can use position restraint on
> molecule 1 and pull the molecule 2 away from molecule 1 in only
> x-direction? Thanks for your inputs in advance.
> -Sudha
>
>
> On Thu, Sep 18, 2008 at 3:36 PM, <nurith_at_rice.edu> wrote:
> Hi,
>
> I am trying to run umbrella sampling on a reaction coordinate
> described as the RMSD w.r.t. some reference structure. Is
> there a way to do it in AMBER, similar to the CONS module in
> CHARMM?
> >From the little documentation there is, I could only find how
> to make distance, angle and dihedral restraints. Can I also do
> RMSD?
>
> Thanks!
> N.
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-- 
Jerome Golebiowski, PhD
LCMBA, team Chemometrics and Molecular Modeling
University of Nice, parc Valrose
06108 Nice Cedex2 France
tel : +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
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