VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Mar 30 2018 - 10:19:32 CDT

Hi Rakesh,

You may need to do energy minimization and equilibrate your coarse grain
system before you start running production run.
Thanks.

Rabeta Yeasmin

On Fri, Mar 30, 2018 at 9:41 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> how about posting questions about NAMD to the *NAMD* mailing list and
> not the VMD mailing list?
>
> axel.
>
> On Fri, Mar 30, 2018 at 9:39 AM, RAKESH <rakeshkrish_at_iitb.ac.in> wrote:
> > Dear all,
> >
> > I have modelled a protein of 160 amino acids and simulated it for few
> 100ns
> > in namd.
> > Then I coarse grained the system using MARTINI and tried it to further
> > simulate for some microseconds.
> >
> > The simulation was running and abruptly got crashed in between during the
> > production run,
> > something like this
> >
> >
> > ERROR: Atom 420 velocity is 25965.1 12571.2 -6373.37 (limit is 1200,
> atom 35
> > of 70 on patch 159 pe 17)
> > ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
> > patch 159 pe 17).
> > ERROR: Exiting prematurely; see error messages above.
> > ERROR: Atom 496 velocity is -25706.5 -12714.7 6397.55 (limit is 1200,
> atom
> > 31 of 67 on patch 158 pe 15)
> > ERROR: Atom 476 velocity is -1050.43 -77.2906 -943.981 (limit is 1200,
> atom
> > 63 of 67 on patch 158 pe 15)
> > ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
> > patch 158 pe 15).
> >
> > Can someone what is the error ??
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>