TCL Scripting for Force Calculations

From: Allen, Caley R (
Date: Mon May 02 2016 - 10:48:56 CDT

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.



Caley Allen, Ph.D.

Postdoctoral Fellow

The Georgia Institute of Technology

Hernandez Research Group

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