[gmx-users] Generate many random configurations

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 5 18:24:27 CET 2014

On Wed, Mar 5, 2014 at 5:32 PM, rankinb <rankinb at purdue.edu> wrote:

> As many of you probably know, genbox may be used to add additional solute
> molecules to a simulation box with a .gro output file containing the
> coordinates of initial and added solute atoms.  Is it possible to do this
> many times (i.e. >1000) with a single output that contains the coordinates
> of all trials?  If not, does anyone have a suggestion as to how to do this?
> I can imagine writing a script accomplish this (outside of GROMACS), but I
> was wondering if there were a simple way to implement this in GROMACS, as
> it
> does most of what I want it to do.

The right approach is a script that calls genbox repeatedly with different
seeds, and which uses trjcat to combine the resulting output. GROMACS aims
to provide UNIX-style components that can be combined to form your
workflow, rather than attempting to anticipate all possible workflows.


> Thanks,
> Blake
> Purdue University
> Department of Chemistry
> Ben-Amotz Lab
> PhD Candidate
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