Re: [AMBER] How to define COM for groups in ASMD

From: Kellon Belfon <>
Date: Tue, 9 Mar 2021 21:37:38 -0500

Hi Matthew,

The form you mentioned first should work for COM distances between two
groups of atoms specified by igr1 and igr2. While the manual does mention
coordinate-averaged position is being used, however, when ir6 =0 (which is
the default) then the averaged position is calculated using center-of mass
averaging. So what you have listed here should work as CoM distance
between the two groups (igr1 and igr2). You need to add the atom numbers to
igr1 and igr2 that correspond to the group.

rk2 = 5000

Also if you are varying the distance over some number of steps (using r2
and r2a) then you will have to define ifvari=1). Check out page 549 in the
manual for more information.

The other form (natural language) is used for sander.

On Sat, Mar 6, 2021 at 3:13 AM Matthew Guberman-Pfeffer <> wrote:

> Dear Amber Community,
> Similar to a recent post, I want to pull apart two proteins by applying a
> distance restraint to their centers of mass. I know that a distance
> restraint of the form
> &rst
> iat=-1,-1
> r2=15.,
> r2a=20.
> rk2 = 5000
> igr1=...
> igr2=…
> /
> would apply to the coordinate-averaged positions of the groups. Would a
> work around to instead use COMs be (I’m not sure what to do with the iat
> variable):
> &rst
> restraint = "distance( COM(...) COM(...) )”
> /
> Or, is there no way to implement this?
> Best regards,
> Matthew
> _______________________________________________
> AMBER mailing list

Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237>  Email:  kellon.belfon.stonybrook.
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Received on Tue Mar 09 2021 - 19:00:02 PST
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