AW: Fixed and SMD atoms

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

        

 

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:52 CST