VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 30 2018 - 09:41:50 CDT

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.