RE: how to get cell vectors in tcl forces script

From: Cosseddu, Salvatore (
Date: Wed Mar 12 2014 - 07:05:43 CDT

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. M?rz 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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