AW: outputting atom coordinated

From: Norman Geist (
Date: Mon Sep 17 2012 - 01:52:28 CDT



Von: [] Im Auftrag
von Jacqueline Schmidt
Gesendet: Sonntag, 16. September 2012 23:17
An: namd
Betreff: namd-l: outputting atom coordinated


Dear Namd users,

I want to use the Tcl Force commands to print the coordinates of a selected
set of atoms onto a separate file. Should I include the tcl force section
before the "run" in namd configuration? or it doesn't matter?


As the namd config file is executed like a script as far as I know, you will
have to put it before the run command, as namd doesn't know at this point
what definitions you entered below.


Second how do I redirect the coordinated into a separate file?


This is a general TCL question. You will find lots of information about that
in the net.

The namd manual or the mailing list will additionally point out how to
access the coordinates of the atoms from the TCL interface.


Thanks! jackie

PS: I need the coordinates more often than what I'd output the dcd. That is
why I am trying to use tclForces!

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