[gmx-users] Error in mdrun

Justin Lemkul jalemkul at vt.edu
Wed Jun 4 14:15:45 CEST 2014

On 6/4/14, 6:47 AM, Praveen Kumar wrote:
> Harshkumar,
> If you are using NPT ensamble, volume will not fix. After some time as box
> length decrease than cut-off, you will get such type of error. You can
> increase number of water molecules or decrease cut-off.

Decreasing the cutoff may "work" to get rid of the error, but there can be 
consequences in the validity of the physics if you make ad hoc changes just to 
get the simulation to run, or run faster...


> On Wed, Jun 4, 2014 at 4:06 PM, Harshkumar Singh <harshsingh2293 at gmail.com>
> wrote:
>> I have been doing simulation of 216 SPC molecules with cubic box dimension
>> 3 nm.I have set the cut off at 1.2 nm but I get this error during mdrun
>> one of the box vectors has become shorter than twice the cut-off or
>> box_yy-|box_zy| or box_zz has become smaller than the cut-off error
>> The box vector is greater than double than twice the cut-off but I don't
>> seem to understand the other possible errors.How can I resolve them?
>> --
>> Harshkumar Singh
>> 2nd Year Integrated MSc Chemistry
>> IIT Bombay.
>> --
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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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