[gmx-users] genbox and martini, ethanol solvent

Pim Frederix pim.frederix at strath.ac.uk
Mon Sep 20 11:26:08 CEST 2010

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?

Thanks very much in advance,

PhD student University of Strathclyde
Pure & Applied Chemistry / Biomolecular and Chemical Physics

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