AMBER Archive (2008)

Subject: AMBER: Re: reaction coordinate in umbrella sampling

From: Sudha Mani Karra (karra.md_at_gmail.com)
Date: Mon Sep 22 2008 - 10:00:42 CDT

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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