[gmx-users] Error during Energy minimization
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
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
School Of Chemistry
"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"
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