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...
-Justin
On Wed, Jun 4, 2014 at 4:06 PM, Harshkumar Singh <harshsingh2...@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
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