From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Oct 22 2013 - 03:37:09 CDT
Hi Mihaela,
try
fixedAtomsCol B
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Dienstag, 22. Oktober 2013 00:33
An: Norman Geist
Betreff: Re: namd-l: Fixed and SMD atoms
Hello,
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,
Mihaela
On Mon, Oct 21, 2013 at 2:37 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> 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: 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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