[gmx-users] About Box VEctor

Justin Lemkul jalemkul at vt.edu
Sat Nov 10 15:00:49 CET 2012

On 11/10/12 8:51 AM, vidhya sankar wrote:
> Dear  Justin Thank you for your Previous Help Reply.
>                                                                                          I am Doing Protein Lipid Tutorial  I Have Done Successive  Shrinking (using inflate script) and EM until i reached APL (66.7 A^2) for  DPPC in protein After Doing Sufficient Em and Shrinking steps  I reaches   box size of 6.81123   6.81123   5.00000
>    At the End of Last EM
>     May it Deviate from initial Box Size  (5 5 5) ?

The initial box size of the DPPC lipids in the tutorial is not 5x5x5.  The x-y 
dimensions are on the order of 6.4 nm, if I recall.  The final structure in the 
tutorial should have similar box vectors, but again I don't know the exact 
values offhand.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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