[gmx-users] Regarding using random seed

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 9 11:07:12 CET 2016

Hi Neha,

You can perform a simulation first, and then extract configurations, which
you simulate with new starting velocities. Alternatively, you can generate
a number of different starting structures using elastic-network modeling,
like with the ElNemo server. Mind to first energy minimize the resulting,
extrapolated structures, as they may be stretchedhere and there.

Hope it helps,


On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <nehachaudhary769 at gmail.com>

> Hello there,
> Can anyone tell me how can I start my MD simulations with different
> starting structure (random seed) for my protein-ligand complex. Can I start
> with different sets of coordinates and velocities? If yes, how?
> Thanks,
> *Neha*
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
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Tsjerk A. Wassenaar, Ph.D.

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