AMBER Archive (2007)

Subject: Re: AMBER: Umbrella sampling

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Oct 26 2007 - 09:11:14 CDT

Jeninha

Can you please email me (not the list) you md.in and maybe your distance
vs time files for a couple of the steps. I might be able to help
a.

Jena M wrote:
> Dear amber users,
>
> I have some questions related with the umbrella sampling method. I want to approach an atom of a ligand (C5) to an atom of a residue (OD1) from a distance of ~6 A to 4 A using a step of 0.2 A to study a reaction mechanism. So, after each equilibration I look for the distance C5-OD1 and subtract 0.2 to obtain the value of r2/r3 to be used in the restraint file for the next production MD. However, at the end of each production MD I always obtain a final structure with a distance C5-OD1 higher than that specified in the r2/r3. For instance, for the third step:
> -Third MD (20 ps) to equilibrate the system
> final distance (C5-OD1)= 5.809
> -Third MD (50 ps) to approach the atoms
> r2/r3=5.609
> final distance (C5-OD1)= 5.625
>
> Then I started the fourth equilibration using the rst file of the third production and I obtained a final distance C5-OD1 of 5.518. In this equilibration I had to use a force of 50 to restraint the heavy atoms otherwise the atoms were separated by a distance higher than 5.625. For the fourth production:
> r2/r3= 5.318
> final distance (C5-OD1)= 5.462
>
> Is it correct the way the way I am doing the umbrella sampling? Is it expected that the value of the distance obtained at the end of each production be different of that specified in r2/r3 ?
> My input is:
> &rst iat=461,569, r1=0.0, r2=5.609, r3=5.609, r4=100.0, rk2=100., rk3=100.,
> iresid=1,
> ATNAM(1)='OD1',
> ATNAM(2)='C5',
> /
> Should I increase the force? I think it is already high…
>
> Thanks in advance
> Jeninha
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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