[gmx-users] strange behaviour of gmx solvent with non standard solvent

Sridhar Kumar Kannam srisriphy at gmail.com
Sun Sep 21 04:16:12 CEST 2014

Hi Gromacs user,

I am trying to solvate a protein (martini coarse-grained) with non-standard
solvent provided here - http://md.chem.rug.nl/cgmartini/index.php/proteins
(water-box-CG_303K-1bar.gro). I am using the below two commands 1. defining
the box size, 2. solvating with gmx-solvent.

gmx editconf -f protein.gro -o protein-box.gro -c -box 7.4 7.4 7.4 -bt cubic

gmx solvate -cp protein-box.gro -cs water-box-CG_303K-1bar.gro -scale 0.21
-o system.gro -p system.top

Changing the box size to 7.5 7.5 7.5 and 7.6 7.6 7.6 is resulting in a very
different solvent density in the system.gro,  than the expected density
from the water-box-CG_303K-1bar.gro.

I could not find any correlation with the box size but I have noticed two
problems at some box sizes.

1. Very high density at some box sizes.
2. The solvent atoms are placed too close to each other at some box sizes.
This is resulting in the failure of minimization at the next stage.

A similar problem related to my 2nd observation is raised here -

The errors can be reproduced by using the files here (Download all the
files of this module
- http://md.chem.rug.nl/cgmartini/index.php/proteins

Any ideas ...?

Than you.

Cheers !!!
Sridhar  Kumar Kannam :)

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