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

From: Seetin, Matthew <>
Date: Wed, 7 Apr 2010 14:50:33 -0400

Symmetric restraints are unnecessary as long as the force constants are symmetric, because it's impossible to have a negative distance between atoms. I would set r1 to 0.0 and r4 to be something much larger than r2/r3, like 100+r2. If you actually are sampling or trying to sample in the neighborhood of r = 0, WHAM will put an infinitely high barrier there, but that's just the the nature of how things work.

--Matthew Seetin

-----Original Message-----
From: on behalf of Matthias Wildauer
Sent: Wed 4/7/2010 2:04 PM
Subject: [AMBER] Umbrella Sampling with distances;setting of r1 and r4 in the restraint
Hello everybody,

i've a question regarding umbrella sampling with distances and further
analysis with the WHAM program of Alan Grossfield.

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,

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?

Thanks for every answer!
Best regards,
Matthias Wildauer, B. Sc.

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Received on Wed Apr 07 2010 - 12:00:06 PDT
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