Re: GBIS and ABF

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Mar 28 2011 - 10:08:00 CDT

Hi Bjoern, use Python or whichever other language you're most confident in
to generate configuration files. You only need to use Tcl if you want to do
things while NAMD is running (i.e. transform the NAMD configuration file in
a script). Otherwise, what works best for you is the best choice.

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Mon, Mar 28, 2011 at 3:45 AM, Bjoern Olausson <namdlist_at_googlemail.com>wrote:

> On Wednesday 23 March 2011 18:10:15 Jérôme Hénin wrote:
> > I recommend some Tcl magic for this, i.e. writing a "template" colvars
> > config file containing macros: keywords that need to be substituted
> > with values. Then in the NAMD config file, some Tcl procedure could be
> > called to read the template, perform macro substitution (using regsub)
> > and write a final colvars config file, which is passed to NAMD.
> >
> Okay, thats pretty much the same what I do with Python and the template
> module. But since I am not as skilled in TCL as in Python I didn't know
> about
> this feature in TCL. But I am _slowly_ getting more and more used to TCL.
>
>
> On Wednesday 23 March 2011 20:17:48 Ajasja Ljubetič wrote:
> > Hi Bjoern,
> >
> > For a quick and dirty solution see
> > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13490.html
> > <http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13490.html>In
> > the meantime have also devised a bit more elegant solution (one that can
> > also use TCL's flow control).
> >
> Sweet, that will do the trick for me (just replacing one variable).
>
> > If you're interested I can post an example tomorrow (when I get back to
> > work).
> >
> Sure I am interested in an elegant solution too.
>
>
> Thanks a lot for your suggestions.
>
> Cheers,
> Bjoern
>
> --
> Bjoern Olausson
> Martin-Luther-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>

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