SMD: Fixing centroid

From: Moumita Saharay (
Date: Tue Dec 14 2021 - 04:18:10 CST

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
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]


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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