[gmx-users] Randomly alter pdb start coordinates

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 25 09:42:54 CEST 2015


On Tue, Aug 25, 2015 at 5:08 AM PER HENRY ANDREAS WITTLER <
17526019 at students.latrobe.edu.au> wrote:

> There is mentioned that for re-running an MD run for better statistics, it
> can be good to change starting coordinates, besides the seed, is there a
> gmx command which is used for randomly change starting coordinates of a pdb
> file?

Not really. You can e.g. generate your solvent box in different ways, but
MD is so chaotic that you really don't need to do this. Look at the time
series of your observable from two runs with different velocities, and
observe that their decorrelation time is much shorter than your
equilibration time.

I need such a command or script for a PBS script which automatically goes
> through all gmx setup commands to start and run an arbitrary number of
> following  MD production runs, assumed that all steps are working. I've
> also made it to replicate and change seeds automatically for velocity
> generation for three seeds, starting automatically. So three tests started
> with one bash script, and one clean-up script resetting everything.

It is generally more efficient to do your preparation (via a script) on
some local resource (or the PBS login node), and transfer only the .tpr
file(s) to run with mdrun on the PBS resource via the PBS submission script.


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