Re: Velocity after heating

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jul 18 2005 - 13:35:44 CDT

Now that I looked at your log file, it seems that maybe you used the
wrong coordinates for your fixed atom pdb? You need to use the
equilibrated coordinates, not the original ones.

On Jul 18, 2005, at 6:56 AM, mustapha.hamdi_at_ensi-bourges.fr wrote:

> Hi all,
>
> I have gradually heated my system over some ps to 300k, and when Iím
> trying to apply position restrained MD using this script:
>
> fixedAtoms on
> fixedAtomsFile fix_mysysteme.pdb ;# only fix backbone.
> fixedAtomsCol B
> fixedAtomsForces on
>
> I have received the following error message (see attached .log file):
>
> ERROR: Atom 3429 velocity is -16402.4 -14246.5 -6641.39 (limit is
> 10000)
>
>
> Did some one know why the velocities exceed its limit and is it
> possible
> to change this limit?
>
>
> Thanks for any help.
>
>
> Mustapha
>
>
> --
> Mustapha Hamdi
> Laboratoire Vision et Robotique
> ENSI de Bourges
> 10 Bd Lahitolle 18000
> Bourges France.
> Tel: (+33) 2 48 48 40 79
> GSM: (+33) 6 24 95 39 53
> Fax: (+33) 2 48 48 40 40
> email:mustapha.hamdi_at_ensi-bourges.fr<position_restrained.log>

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