AW: how to get cell vectors in tcl forces script

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Mar 12 2014 - 09:59:12 CDT

You need to try. The output command will just write a set of restarts with
the specified name, so hitting:

 

output test

 

should result in the following files being created:

 

test.coor

test.vel

test.xsc

 

The question is just if the output command is available within TclForces.

 

Norman Geist.

 

Von: Thomas Evangelidis [mailto:tevang3_at_gmail.com]
Gesendet: Mittwoch, 12. Mrz 2014 15:27
An: Cosseddu, Salvatore
Cc: Norman Geist; namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: how to get cell vectors in tcl forces script

 

Hi Norman & Salvatore,

I also thought about reading in the .xsc file but that would slow down the
simulation. Fortunately, the cell vectors do not change drastically - and
precision is

 unnecessary in my case- therefore lowering too much restartfreq is not
needed.

Norman can you give an example of using the output command within a
jobscript file? I don't understand how you can write restart files more
frequently than restartfreq does.

thanks,

Thomas

 

On 12 March 2014 16:01, Cosseddu, Salvatore <S.M.Cosseddu_at_warwick.ac.uk>
wrote:

Hi Norman,

 

This is what I usually do, I set restartfreq conveniently. To be honest I
don't know either about "output" command within tclforces.

 

Best wishes

Salvatore M Cosseddu

  _____

From: Norman Geist <norman.geist_at_uni-greifswald.de>
Sent: 12 March 2014 12:54
To: Cosseddu, Salvatore

Cc: Namd Mailing List
Subject: AW: namd-l: how to get cell vectors in tcl forces script

 

Yes, I mean I dont know if the output command works from TclForces. He
need to try, otherwise he would have to set the restartfreq suitable for his
needs.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Cosseddu, Salvatore

Gesendet: Mittwoch, 12. Mrz 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}

CHECK!!!"

        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: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
Norman Geist <norman.geist_at_uni-greifswald.de>
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

 

Hi,

 

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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Thomas Evangelidis
Gesendet: Dienstag, 11. Mrz 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
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
 
 
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University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
 

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