VMD-L Mailing List
From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Mar 30 2018 - 10:19:32 CDT
- Next message: Peter Mawanga: "Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes"
- Previous message: Axel Kohlmeyer: "Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation"
- In reply to: Axel Kohlmeyer: "Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
>
>
- Next message: Peter Mawanga: "Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes"
- Previous message: Axel Kohlmeyer: "Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation"
- In reply to: Axel Kohlmeyer: "Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]