On 7/29/13 2:12 PM, Scott Pendley wrote:
Thank you, Justin. I am using gromacs version 4.5.5 and have attached .mdp
file. I followed your advise and pointer to trouble shooting the system
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and decomposed the energy to find potential sources for the problem. The
simulation ran for 978 ps, the total energy changed from approximately
-13000 kj/mol to -15000 kj/mol and plateau'ed out around 900 ps without a
big energy blow-out. The majority of the change in energy was from the LJ
contribution which is the expected source with the disappearing atoms of my
ligand. Of more concern is the change in box coordinates/shape. The
simulation cell starts with dimensions 9.45nm x 9.45nm x 9.45nm and ends at
2.8 x 2.8 x 45.8 nm which does seem to give rise to the error that I
originally noted. While some change in volume and cell dimensions is
expected, these changes seems to be a focused solely on expanding along the
Z-coordinate. Is there any way to constrain the ratio of x:y:z coordinates
during npt simulations or do you know of something that I may be missing in
my simulations?
The magnitude of change you're seeing suggests extreme instability and thus
there is no real "hack" to simply "make it work." Isotropic pressure coupling
is normally sufficient for this purpose, but something seems to be going very
wrong in your system. The complete .mdp file, and a description of what your
ligand is (or at least how big) would be helpful. You've got a very large box
for what one would normally consider a "ligand."
-Justin
Thank you,
Scott
On Wed, Jul 24, 2013 at 4:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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<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<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
--
==============================**====================
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Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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706-7441
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Justin A. Lemkul, Ph.D.
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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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