From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Oct 21 2013 - 01:37:28 CDT
For fixing atoms, you only need that part:
set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top " name CG"]
$fixedatom set beta 1
$allatoms writepdb common/watergraphite.ref
What do you need all the rest for?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Mihaela Drenscko
Gesendet: Samstag, 19. Oktober 2013 21:17
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Fixed and SMD atoms
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
files):
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,
Mihaela
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