[gmx-users] Error in mdrun
jalemkul at vt.edu
Wed Jun 4 14:15:45 CEST 2014
On 6/4/14, 6:47 AM, Praveen Kumar wrote:
> 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>
>> 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.
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