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

From: Matthias Wildauer <amber.wildauer.org>
Date: Wed, 7 Apr 2010 20:53:53 +0200

Thank you both very much for the fast answers!

On 04/07/2010 08:04 PM, Matthias Wildauer wrote:
> 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, right?
>
> 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?
>
> Best regards,
> Matthias Wildauer, B. Sc.
>
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Received on Wed Apr 07 2010 - 12:00:09 PDT
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