AW: Fixed and SMD atoms

From: Norman Geist (
Date: Tue Oct 22 2013 - 03:37:09 CDT

Hi Mihaela,




fixedAtomsCol B


Norman Geist.


Von: Mihaela Drenscko []
Gesendet: Dienstag, 22. Oktober 2013 00:33
An: Norman Geist
Betreff: Re: namd-l: Fixed and SMD atoms



OK, I eliminated the Extra Parameters section from the configuration file
(the SMD part), but I kept The Fixed Atoms Constrains section:

# Fixed Atoms Constrains
if {1} {
fixedAtomsFile watergraphite.ref

I must have done something wrong, because my two sheets of graphite
"slided", after I run the simulation.

What could be the problem?

Thank you,





On Mon, Oct 21, 2013 at 2:37 AM, Norman Geist
<> wrote:

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: [] Im Auftrag
von Mihaela Drenscko
Gesendet: Samstag, 19. Oktober 2013 21:17
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

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,





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