Re: [AMBER] distance restraint, recenter

From: case <>
Date: Thu, 18 Nov 2010 09:04:30 -0500

On Thu, Nov 18, 2010, Nadine Utz wrote:

> I am doing umbrella sampling with a distance restraint between two atoms

> Does anybody know if periodic boundary cond. are considered as well for
> the restraints?

No, the distance restraint code doesn't know about periodic boundaries.

> E.g. if I force the distance to be 10 A by applying a
> force constant, and the molecule jumps in the next box,

You need to turn off iwrap (set it to the default value of zero). Then there
should be no "jumps" between frames.

...good luck....dac

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Received on Thu Nov 18 2010 - 06:30:03 PST
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