AW: Fixing atoms while equilibration

From: Norman Geist (
Date: Mon Sep 01 2014 - 02:26:11 CDT

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Siva Dasetty
> Gesendet: Samstag, 30. August 2014 03:12
> An:
> Betreff: namd-l: Fixing atoms while equilibration
> Dear All,
> I am doing an energy minimization of graphene in implicit solvent by
> fixing all graphene atoms using fixedAtoms=on in NAMD version 2.10b1.
> As expected all the energies are 0 in my output log file as I excluded
> all bonded and non bonded interactions, however temp and tempavg seems
> to have this huge number “999999999.99999”. Can someone please explain
> this?


as the minimizer works at zero Kelvin and you have temperature, I think you
did something wrong with your script.
Also, what else is in your system in order to be minimized if you graphene
is fixed?

Norman Geist

> Thanks,
> Siva

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