Re: SMD: Fixing centroid

From: Anup Prasad (
Date: Tue Dec 14 2021 - 05:02:53 CST

Hi Dr. Moumita,
I don't think that there is any straightforward command for fixing the
centroid of a group of atoms. Instead of it you can try the "distance
colvar" module. You have to calculate the centre of mass (com) of the group
of atoms and create the dummy atom at this com. Then apply distance colvar
between "group of atoms" and "dummy atoms" along with SMD simulation. Fix
the dummy atom in SMD instead of a group of atoms.


On Tue, 14 Dec 2021 at 15:52, Moumita Saharay <>

> Dear all,
> I want to perform a constant velocity pulling experiment using
> Steered Molecular Dynamics (SMD). I used the following TCL
> script to mark the fixed and SMD atoms. It works well when there is
> only one atom to be fixed. But I want to fix the centroid of a collection
> of
> CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480.
> How do I do that ? Please help me to resolve this issue.
> TCL script:
> set allatoms [atomselect top all]
> $allatoms set beta 0
> set fixedatom [atomselect top "resname GLU and resid 203 and name CA"]
> $fixedatom set beta 1
> $allatoms set occupancy 0
> set smdatom [atomselect top "index 10525"]
> $smdatom set occupancy 1
> $allatoms writepdb smd_step5_01.ref
> set smdpos [lindex [$smdatom get {x y z}] 0]
> set fixedpos [lindex [$fixedatom get {x y z}] 0]
> vecnorm [vecsub $smdpos $fixedpos]
> Thanks,
> Moumita
> --
> Dr. Moumita Saharay
> Assistant Professor,
> Department of Systems and Computational Biology,
> School of Life Sciences,
> University of Hyderabad,
> Gachibowli, Hyderabad, India

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