Re: Tcl, minimization and MD (Warning: I am a lazy ignorant)

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 20 2006 - 10:40:52 CDT

Dear Miro,
is there any particular reason for you to not want to minimize before
you start your dynamics? This is almost certainly the problem, but I do
not understand why you don't want to perform a short minimization prior
to your run if you have changed the topology in the meantime (which it
sounds like you did, if you were running psfgen in the middle).
Peter

Edelmiro Moman wrote:
> Hello,
>
> I do not know a work of Tcl scripting (or almost any other scripting
> language). In consequence, when I try to use a modified version of the
> NAMD sample.conf file, I get all kind of warning messages (if I use
> constraints, they tell me about bad geometries; otherwise they
> complain about high velocities) and the simulation is immediately
> aborted. I (ignorant) suspect that NAMD is starting directly with the
> MD simulation without doing a previous minimization (as I would wish).
> This is the relevant (I guess) fragment of the file:
> ______________________________________________________________
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {0} {
> minimize 100
> reinitvels $temperature
> }
>
> run 50000 ;# 100ps
> ______________________________________________________________
>
> First silly question: Am I right (by chance)?
>
> Second silly question: What can I do?
>
> Some clues: If the system has been previously minimized the simulation
> uses to runs uneventfully; but (!) Autopsfgen removes the hydrogens
> from my system and add them again, as a result of which the geometry
> of the prolines uses to be completely wrong and that takes me to the
> original problem.
>
> Kind regards,
>
> Miro
>
> P.S.: I am not as lazy as I am ignorant. However, as I am aware that
> my messages can hurt certain sensibilities, I have include a warning
> in the subject so that sensitive people do not have to read them.
> About unnecessarily increasing network traffic, I am very sorry about
> that and I plan to punish myself as soon as I can think of a suitable
> way of doing it.
>
>

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