[gmx-users] FATAL ERROR

Rahul Karyappa r.karyappa at ncl.res.in
Fri Sep 23 13:49:06 CEST 2005

Hi amol ,
   actually the problem is woth your topology i.e. you need to minimize the energy of your structure. Then only you can run the mdrun. I have also faced the same problem previously.
Best of luck.
Rahul Karyappa
NCL, Pune

-- Original Message --
From: "Amol D. Atre" <ssb4 at udct.org>
To: gmx-users at gromacs.org
Date: Fri, 23 Sep 2005 12:00:17 +0530 (IST)
Subject: [gmx-users] FATAL ERROR
Hello all,
While running pdb2gmx for cpeptide.pdb included in tutor/gmxdenmo folder I
am getting,
FATAL ERROR: One of the box vectors is shorter than twice the cut-off
length. Increase the box size or decrease rlist.
Can anybody throw some light on this?
OS: Linux Fedora Core
Command line: pdb2gmx -f cpeptide.pdb -o conf.gro -p topol.top -i posre.itp
Thanking in advance.
Amol D. Atre.
Lab No.A002,
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
Matunga(E), Mumbai-400019.
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