Fixed and SMD atoms

From: Mihaela Drenscko (
Date: Sat Oct 19 2013 - 14:16:47 CDT

I have two sheets of graphite and I want to keep the atoms in fixed
positions. In the NAMD tutorial I found the following script for this
purpose (which I modified slightly according to the requiremnts of my

set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top " name CG"]
$fixedatom set beta 1
$allatoms set occupancy 0
set smdatom [atomselect top " name CG"]

 $smdatom set occupancy 1
 $allatoms writepdb common/watergraphite.ref
set smdpos [lindex [$smdatom get {x y z}] 0] set fixedpos [lindex
[$fixedatom get {x y z}] 0] vecnorm [vecsub $smdpos $fixedpos]

I get this error:

domain error: argument not in valid range

How do I fix it?

Thank you,


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:47 CST