[gmx-users] Error during Energy minimization

[Deepak Ojha]

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"