[gmx-users] genconf

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 9 19:54:10 CET 2012

saly jackson wrote:
> Hi all
> I used genconf and genbox command as the following:
> genconf -nbox 50 50 40 -f H.gro -nmolat 100  -o H-box.gro

How many molecules are in H.gro and H-box.gro?  Is H.gro a single molecule?

> genbox -cs H-box.gro -nmol 100000 -box 100 100 100  -p topol.top -o 
> H-box_new.gro

You've been advised again and again that building enormous systems in one step 
will not work.  This is not a robust approach, as your computer clearly doesn't 
have the memory to handle it.  Before you were trying to add 80000 molecules, 
now 100000 certainly won't work.  I doubt the combination of -cs and -nmol is 
even sound in the first place.

Is there a particular reason you feel you need to construct a system containing 
100000 molecules?  Will a smaller, more manageable, system not suffice?


> But I received:
> Reading solvent configuration
> "Great Red Owns Many ACres of Sand "
> solvent configuration contains 600000 atoms in 100000 residues
> Killed
> Would you please help me?
> Thanks alot
> Regards
> Saly


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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