group selection in TCL script for use in NAMD

From: Allen, Caley R (
Date: Wed Jul 27 2016 - 13:35:05 CDT

Greetings NAMD experts.

I have a large pdb file composed of a lipid bilayer, protein, and ionized TIP3P water. I am attempting to execute a steered MD calculation wherein I steer the protein by COM away from the lipid bilayer defined by COM.

I am calling a "smdforce.tcl" script from the smd.namd file (configuration file).

In the smdforce.tcl script I have the following lines:

set lip [addgroup {9500 9501 9502 ...........9768}]

set prot [addgroup {1 2 3 4 .......674}]

Then I set the freq, force, etc... further down in the script. I using the addgroup command in order to determine the COM for the defined groups, which I then use in the steering.

Here is my question/issue. The above works if the groupIDs are unique. Meaning that the protein, water, and bilayer do not have common resids. This is the issue. The resids are going to shared.

So how do I make the corresponding selections in the tcl script for COM of the protein and COM of the bilayer? I know how to execute the tcl file in the NAMD configuration file. There is a limited language for use in NAMD (versus use in VMD), so I do not know what to do.

Any help is substantially appreciated. If you could provide an example I would greatly, greatly appreciate it.

Please help.



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