[AMBER] distance restraint, recenter

From: Nadine Utz <nadine.mmb.pcb.ub.es>
Date: Thu, 18 Nov 2010 14:35:29 +0100

I am doing umbrella sampling with a distance restraint between two atoms
in 2 different molecules. When I am doing MD simulations with dist.
restraint for the different windows and increase the distance, one
molecule "jumps" in the next box, which is normally not a problem due
to periodic boundary cond.

Does anybody know if periodic boundary cond. are considered as well for
the restraints? E.g. if I force the distance to be 10 A by applying a
force constant, and the molecule jumps in the next box, which distance
is considered by sander? The imaged one which is around 10 A, or the one
between 1 molecule in 1 box and the 2nd molecule in the 2nd box, which
is far away from 10 A?

As I fear the latter one is the case, is there a way to recenter
everything during or after each simulation, so that no jumps take place?

Thank you very much for any help and best regards,


Dr. Nadine Utz
Molecular Modelling & Bioinformatics Group
Institute for Research in Biomedicine (IRB) Barcelona

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Received on Thu Nov 18 2010 - 06:00:09 PST
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