Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint

From: case <>
Date: Wed, 7 Apr 2010 14:51:06 -0400

On Wed, Apr 07, 2010, Matthias Wildauer wrote:
> The WHAM program assumes that the restraint potentials are harmonic, so
> r3 should be set to r2, and r1 & r4 should be set far away from r2/r3.
> If you have angular restraints, then it's of course no problem to set
> them to negative values (like e.g. r1= -60, r2=60, r3=60, r4=180). But
> if you regard distance restraints you shouldn't set r1 to a negative
> value in order to have always the same distance r1 & r4 values to r2/r3,
> right?

Correct; if you are looking at atom-atom distances, then the distances
will never get close to zero (because of LJ terms), and hence the exact
value of r1 becomes irrelevant; zero should be fine.
> A example:
> I'd like to perform sampling with 4.0, 4.5, 5.0, ... 12.5 Angstroms. At
> the moment my values for rX are:
> 4.0: r1=0 r2=4.0 r3=4.0 r4=8.0
> 4.5: r1=0 r2=4.5 r3=4.5 r4=9.0
> 5.0: r1=0 r2=5.0 r3=5.0 r4=10.0
> ... (r4 are always of the double of r2/r3)
> Could this cause (real) problems with the free energies, because the
> harmonic potentials are "soften" with larger target-distances? If so,
> how should i set the r1/r4 values?

Why not just set r4 to 999. for all restraints? All you need is a value that
will never be exceeded.


AMBER mailing list
Received on Wed Apr 07 2010 - 12:00:07 PDT
Custom Search