[gmx-users] Error during Energy minimization

Deepak Ojha alwaysinthemind at gmail.com
Sat Aug 2 00:59:11 CEST 2014

Dear Gmx Users

I am trying to do a simulation of 108 methanol molecules using
gromacs.Instead of generating gro file using pdb2gmx
I used pdb file and manually generated a topology file using virtual
chemistry.org <http://virtualchemistry.org>. The box size is around 20A
which consists
of the entire  system. However when I tried to do energy minimization I get
the error which says

"The cut-off length is longer than half the shortest box vector or longer
than the smallest box diagonal element"
I am not sure if the box length being not specified in PDB file is the
source of error.I gave the very low values of r_cut
but I am still getting same error.

Where do I give the box length information if using  a PDB file instead of
gro file.

DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"

More information about the gromacs.org_gmx-users mailing list