AW: how to get cell vectors in tcl forces script

From: Norman Geist (
Date: Wed Mar 12 2014 - 07:54:50 CDT

Yes, I mean I don’t know if the “output” command works from TclForces. He
need to try, otherwise he would have to set the restartfreq suitable for his


Norman Geist.


Von: [] Im Auftrag
von Cosseddu, Salvatore
Gesendet: Mittwoch, 12. März 2014 13:06
An: Namd Mailing List
Betreff: RE: namd-l: how to get cell vectors in tcl forces script


Dear Norman and Thomas,


It works also within tclforces. You must be ready to a slight loss of
performance for the additional I/O work. Anyway the following procedure has
been tested and have worked fine for me since version 2.8. Hope it will help



proc readcell {xscfile} {


    if {[catch {open "${xscfile}" r} xsc]} {

        puts stderr "ERROR opening ${xscfile}


        exit 1



    set in [read $xsc]

    set bcell [list [lindex $in 28] [lindex $in 32] [lindex $in 36]]

    print "readcell: read cell, at step [lindex $in 27] was $bcell"

    close $xsc

    return $bcell




simply usage:


set boxcell [readcell <xsc filename>]


Best regards

Salvatore M Cosseddu



From: <> on behalf of
Norman Geist <>
Sent: 12 March 2014 07:29
To: 'Thomas Evangelidis'
Cc: Namd Mailing List
Subject: AW: namd-l: how to get cell vectors in tcl forces script




I was also searching for such a command, but the only way you are currently
able to do it, seems to be using the “output” command to write a set of
restarts and read the box info out of the xsc file. No idea if this is also
possible within TclForces, but its working from jobscript context. Also,
just to mention it, the only way currently to “set” the box during
simulation is by loading dcd frames with the “coorfile” command.


Norman Geist.


Von: [] Im Auftrag
von Thomas Evangelidis
Gesendet: Dienstag, 11. März 2014 21:14
An: namd-l
Betreff: namd-l: how to get cell vectors in tcl forces script


Dear NAMD community,

Is it possible to get the current unit cell vectors on the fly from within a
tcl forces script?

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

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