[gmx-users] genbox and martini, ethanol solvent

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 20 14:25:01 CEST 2010

Pim Frederix wrote:
> Dear users,
> I'm trying to create a box with a number (64) of small peptide molecules
> (diphenylalanine) solved in ethanol for a Gromacs run with the Martini
> coarse-grain force field. I've created the box with the solute with the
> genbox -ci command: genbox -ci FFMM_cg.pdb -nmol 64 -box 5 5 5 -o
> FFMM_box.gro. This all seemed to work fine and I confirmed that it worked in
> VMD.
> However, when I try to fill the box with ethanol, this gives problems: genbox
> -cp FFMM_box.gro -cs ethanol_cg.pdb gets stuck at "Reading solvent
> configuration "" solvent configuration contains 1 atoms in 1 residues" (no
> error message, but just stops). 1 atom in 1 residue is correct for my pdb
> file, since ethanol is represented by 1 atom in Martini.
> I have tried to circumvent this problem by using the ci option again to add
> ethanol molecules 1 by 1. This kind of works, but if I try it for too many
> molecules (nmol >15000) it crashes as well with the message 'killed'. Also
> solving in ethanol that's not converted to coarse grain gets stuck (except
> from that it says 9 atoms in 1 residue). I have tried to solve it in the
> spc216 water, this works, so there must be something wrong with my pdb file
> for the solvent. I can see in other solvent gro/pdb files that there are
> usually a lot of solvent molecules in 1 file. Why is that and what can I do
> to make the ethanol box?

Using -ci -nmol is prone to running out of memory, which is probably what's 
happening in your case.  If you use genbox -cs, the configuration in the solvent 
coordinate file is expected to contain multiple atoms, or at the very least, 
multiple molecules.  You can generate a box of CG ethanol using genconf -nbox 
(to make a grid), then equilibrate.  Use this configuration as your solvent 
using genbox -cs.


> Thanks very much in advance,
> Pim PhD student University of Strathclyde Pure & Applied Chemistry /
> Biomolecular and Chemical Physics


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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