[gmx-users] A problem about genbox

Rahul Karyappa r.karyappa at ncl.res.in
Wed Oct 19 06:03:05 CEST 2005

Dear Sir,

     It is not the gmx problem. May be the problem
is with your machine memory. I am able to create a box of size 14 x 14
x 14 (nm). It works fine. I hope it helps you a bit.

Rahul Karyappa

NCL, India
-- Original Message --
From: <zhengbs at jlu.edu.cn>
To: <gmx-users at gromacs.org>
Date: Wed, 19 Oct 2005 00:12:58 +0800
Subject: [gmx-users] A problem about genbox
Dear gmx-users:
am using genbox to solve a protein modeled by modeller.After pdb2gmx
and editconf,there are 335 residues with 3204 atoms,and box size is
6.103 * 6.196 * 6.546.Then i " genbox -cp out -cs -p APE1547LID -o b4em
",when it progressed to
" GRoups of Organic Molecules in ACtion for Science
  Containing 3204 atoms in 335 residues
  Initialising van der waals distances...
  Reading solvent configuration
  solvent configuration contains 648 atoms in 216 residues

",the cursor is flashing but program was seemed not to move on.Is it
too big for gmx to generate a box for this protein,or it will take a
long time?
Thanking in advance
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