On 7/24/13 4:33 PM, Scott Pendley wrote:
I am fairly new to gromacs and I am trying to run a thermodynamic
integration simulation of a ligand disappearing in a box of octanol at a
single set lambda point. I have previous successful nvt and npt runs of
this system. When I have added the free energy portions to the input file,
I get the following error:
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
This seems unusual. The box dimensions are 9.45 nm x 9.45 x 9.45 nm so
that is fairly large even accounting for some shrinkage with a disappearing
ligand.
The available information suggests the system has become unstable and is
imploding. See general troubleshooting information at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.
Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2,
rcoulomb=1.2. Doubling any of them would still be less than 3 nm which is
significantly smaller than the box size. Is there anything I am missing or
any suggestions that others can give me?
I wouldn't mess with the cutoffs; they're an essential part of the force field.
For further diagnostics, please consider the points above and provide your
.mdp file and Gromacs version.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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