[gmx-users] Randomly alter pdb start coordinates

PER HENRY ANDREAS WITTLER 17526019 at students.latrobe.edu.au
Tue Aug 25 05:08:24 CEST 2015

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?

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.


Henry Wittler

Phd in Molecular modelling group (Brian J. Smith)
Department of Chemistry, La Trobe University, Melbourne, Australia
Tel: 0432901627

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