From: Mithun Biswas (mithun_at_theochem.uni-frankfurt.de)
Date: Thu Jul 26 2012 - 08:21:23 CDT
Dear all,
I still cannot get NAMD to write the output coordinates from within the
tclforces script. The "output" command works from outside the tclforces
script though. Is it a known issue ? Please comment. Thanks.
if {abs($phi) < 160} {
set t [getstep] ; #t is in 2fs steps
print "The current time is $t"
output try <<<<< without this line tclforces works fine
print "KILLING NAMD "
exec kill $process
}
Regards,
Mithun
On 07/19/12 17:26, Mithun Biswas wrote:
> Hi,
>
> I want to write a tcl script which checks a certain dihedral angle and
> when the dihedral angle is more than some value, say 20 deg, stops the
> simulation. Then I restart the simulation with a different parameter
> set. To do this I have to mention in the script that on fulfilling the
> angle criteria NAMD should save the current coordinate, velocity etc.
> and stop. So, I added a few lines to my usual namd conf file :
>
> tclForcesScript {
>
> set aid1 907
> set aid2 908
> set aid3 911
> set aid4 914
>
> addatom $aid1
> addatom $aid2
> addatom $aid3
> addatom $aid4
>
> proc calcforces {} {
>
> global aid1 aid2 aid3 aid4 phi
>
> loadcoords p
> print $aid1
> set phi [getdihedral $p($aid1) $p($aid2) $p($aid3) $p($aid4)]
> print "phi=$phi"
> if {$phi > 20} {
> set t [getstep] ; #t is in 2fs steps
> print "The current time is $t"
> output "lastframe_azodna14"
> exit
> }
> }
> }
>
> On running the script, NAMD does not save the output files and exit
> but seems to be stuck. So, I get the following :
>
> **************************
> TCL: 907
> TCL: phi=-179.990377212
> ENERGY: 8 2775.9529 1775.0256 670.5433
> 0.0000 -3419.6739 .....
>
> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 7.47036e+07 TO 74703.6
> TCL: 907
> TCL: phi=179.950813637
> TCL: The current time is 9
> TCL: Writing to files with basename lastframe_azodna14.
> ***************************
>
> Any help is appreciated.
>
> Regards,
>
> Mithun
>
>
-- Dr. Mithun Biswas Institut für Physikalische u. Theoretische Chemie Goethe-Universität Max-von-Laue-Str. 7 60438 Frankfurt am Main Phone: +49 69 798 29030
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