Re: TCL Scripting for Force Calculations

From: Jérôme Hénin (
Date: Mon May 02 2016 - 11:37:19 CDT

Hi Caley,

This sounds like it would be easier to do with the collective variables
module. You can define your sets of atoms by flagging them in a PDB file,
or based on residue and atom names, or with a GROMACS-format index file if
you happen to use those. Then steered MD is implemented as a moving
harmonic bias. If you want a custom algorithm, you can Tcl-script your own
colvar bias:


On 2 May 2016 at 17:48, Allen, Caley R <>

> Good evening NAMD Community.
> I am familiar with and have executed steered molecular dynamics
> simulations before using single atom sites for the anchor cite and pulling
> cite. I have a TCL script written for use with NAMD to do just this.
> Currently I have been trying to do something a little different. I am
> currently trying to steer a polypeptide from a surface by using center of
> masses instead of single atoms (using and adaptive SMD). I know how to
> determine the center of masses for the surface, and for the polypeptide.
> However, I do not know how to incorporate these center of masses into the
> TCL script. I know NAMD provides TCL scripting interface in a limited
> manner. I have tried to use the "TCL Forces and Analysis" webpage for help,
> but I am not getting anywhere. I know I can use addgroup, but how do I list
> the surface (and like wise for the polypeptide)?
> Maybe I am missing something simple.
> Any help would be greatly appreciated.
> Thank you in advance.
> Cheers,
> Caley
> Caley Allen, Ph.D.
> Postdoctoral Fellow
> The Georgia Institute of Technology
> Hernandez Research Group

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