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

From: Matthias Wildauer <amber.wildauer.org>
Date: Wed, 7 Apr 2010 20:04:45 +0200

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 - 11:30:06 PDT
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