AMBER Archive (2007)

Subject: AMBER: Distance restraint to centre of mass

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Fri Mar 30 2007 - 16:41:32 CST

Hi Everyone,

I was hoping to use a distance restraint in an MD simulation where
certain small groups of atoms are restrained away from the centre of
a protein (ie. I want them to experience a radially outward force).
My guess is that this could be accomplished by setting nmropt=1 and
defining a restraint (DISANG) file where each small group is
restrained to a certain distance larger than the protein's radius
away from the protein's centre of mass. The centre of mass could be
represented as the centre of mass of the set of all protein C-
alphas. The only problem I see with doing this is that the igr1 and
igr2 group definitions only accept groups of a maximum size of 200
atoms and even small proteins have more C-alphas than 200. Is there
any way to increase the size of the groups allowed? Is there another
way to access the centre of mass of a protein for a restraint? I
would greatly appreciate any advice anyone can give.

Thanks!

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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