[gmx-users] Box dimension size errors in MARTINI soft core simulation

Justin Lemkul jalemkul at vt.edu
Mon Jul 29 22:39:52 CEST 2013

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

The mailing list does not accept attachments.  Please either copy and paste its 
contents or provide a link from which it can be downloaded.

> 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."


> Thank you,
> Scott
> On Wed, Jul 24, 2013 at 4:59 PM, Justin Lemkul <jalemkul at 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
>>> 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
>> --
>> ==============================**====================
>> 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
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>> ==============================**====================
>> --
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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

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


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