From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 05 2010 - 07:54:27 CDT
On Mon, Apr 5, 2010 at 7:33 AM, Aditya Ranganathan <aditya.sia_at_gmail.com> wrote:
> I`m running an all atom simulation (NVT ensemble) to study the interpeptide
> interaction between ACTH and Beta Endorphin chains. I would like to know
> about the value of the timestep which would be suitable for the same. I
> generally use timestep 2fs for all my simulation. However, I would like to
> know if I can use larger values of timestep, say 3fs. Will doing so cause
> instability or lead to a decrease in accuracy.
> I would like to try a timestep of 3fs as it directly gives a speedup in the
> simulation and allows me to access longer simulation times. What dictates
> the length of the timestep in any simulation? Is any timestep more than 2fs
> not recommended?
if you don't know the answer to this question yourself, you should
not run MD simulations. please pick up a text book on MD and/or
numerical integration and learn about these issues. many even
have detailed error analysis.
> Thanks ,
> Srivastav Ranganathan
> Junior Research Assistant,
> IIT Bombay
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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