You can do as suggested below, but if you need iwrap turned
on, you can define both molecules to be treated as one molecule
in the iwrap process. This is described here:
http://archive.ambermd.org/201006/0452.html
--Niel
________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Thursday, November 18, 2010 7:04 AM
To: AMBER Mailing List
Subject: Re: [AMBER] distance restraint, recenter
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 18 2010 - 07:00:03 PST
