Re: AMBER: Umbrella sampling

From: <>
Date: Fri, 26 Oct 2007 19:08:09 +0200

you can not expect you final value to be perfectly indentical to the minimum of
the distance restraint potential. Your US simulation puts a harmonic potential
on a given distance. With the temperature, this distance can however vary (you
can see it by dumping the instantaneous value and checking that is it indeed

The best that you can expect is that your *average* value during the MD equals
your desired value.

Anyway, your input looks fine.
For me your umbrellan sampling is OK. But maybe I missed something !
Good luck


Selon Jena M <>:

> 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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Jérôme Golebiowski, Ph D.
Lab CMBA, University of Nice Sophia Antipolis
06108 nice cedex 2
tel: +33 (0)4 92 07 61 03
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Received on Sun Oct 28 2007 - 06:07:40 PDT
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