Re: problem in restarting

From: Axel Kohlmeyer (
Date: Thu Apr 14 2011 - 08:29:24 CDT

On Thu, Apr 14, 2011 at 3:11 AM, ipsita basu <> wrote:
> Hi all,
>         Sorry to bother you again.
> But I've a system containing more than 1 lakh atoms including lipids

i don't think you will find too many people on this
list knowing that 1 lakh is 100,000. it might be better
to stick to a more common numbering system. ;)

> and protein, this is minimized for 500,000 steps. If I continue the

500,000 minimization steps is pointless.

if you do have a very high potential energy system, it is
better to minimize for a smaller number of steps, do a
few MD steps and then minimize again.

> job from minimization to heating and then equilibration, the job is
> running without any problem, but if the job is aborted or have to kill
> for any reason and want to restart it again from equilibration or
> heating, then the job is aborted giving the error : atom moving too
> fast, simulation become unstable. But if I again rstart from
> minimization ( even only for 1000 steps) this is running. This is
> really a problem. Can you please help in finding the reason behind
> this? Any kind of help will be appreciated.

you are likely not restarting correctly. impossible to tell
without more information, though.


> Thanking you,
> Ipsita Basu
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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