RE: Velocity after heating

From: wmsmith (wmsmith_at_csupomona.edu)
Date: Mon Jul 18 2005 - 13:04:14 CDT

I had the same problem when trying to run a solvated system that had not
been equilibrated after solvation. I also had the error occur when I applied
very large forces in an SMD simulation.
    In the former case, my guess was that water molecules were placed too
close to the protein during solvation. Equilibrating the system fixed the
problem.

>===== Original Message From mustapha.hamdi_at_ensi-bourges.fr =====
>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

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