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

From: moman_at_titus.u-strasbg.fr
Date: Wed Jun 21 2006 - 03:32:52 CDT

Thanks a lot to Mark, JC and Pedro for given me the right (and expected)
anwser.

Pedro: I have gone once more (quickily, I must confess) throgh the NAMD
tutorial (namely the las chapter as you suggested), but I could not find
an explicit anwser to my (obvious) question:

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/

Surely it is somewhere there, but sitll I can no find it. Never mind.
Thanks a million.

Thaks to Peter as well for always being so regardful and helpful. However,
you got everything this time wrong (mea culpa!). This was not a troll. I
just allowed myself to use a little bit of irony (about last week's
friendly controversy) WHILE asking a honest question AND making you note
what it might be a little bug in the VDM autopsfgen (remarkable) feature:
it seems it systematically asigns wrong coordinates to proline hydrogens
(it removes them from the original file and add them again). I tried a
couple of different protein files generated/converted with either
OpenBabel, SPDBV and MOE and got similar results (wrong geometries) for
the prolines.

This only shows the point that I wanted to highlight with my irony: we are
all (kind of) human ;-) and we are all in the same boat, aren't we?

Cheers,

Miro

> Also... while I did get a chuckle out of the rest of your message, I
> would recommend not feeding the troll. Even he would agree that it is
> better for you to come with what you know and an open mind, than to be
> unduly self deprecating.
> 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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