[gmx-users] Error during Energy minimization

Justin Lemkul jalemkul at vt.edu
Sat Aug 2 01:39:22 CEST 2014

On 8/1/14, 6:59 PM, Deepak Ojha wrote:
> 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.

The box vectors in a PDB file are listed on the CRYST1 line.  Only having 108 
molecules will give rise to the problem because the box is too small to be 
simulated with sensible cutoffs.  Build a larger box with more molecules in it, 
such that the shortest box vector is (at bare minimum) twice the length of the 
longest cutoff.  Cutoffs are essential elements of the force field, so don't 
change those just to get around the problem.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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