VMD-L Mailing List

From: Allen, Caley R (caley.allen_at_chemistry.gatech.edu)
Date: Sun May 01 2016 - 19:54:09 CDT

Good evening VMD 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. 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