[gmx-users] About Box Vector

Justin Lemkul jalemkul at vt.edu
Sat Nov 10 15:37:54 CET 2012

On 11/10/12 9:34 AM, vidhya sankar wrote:
> Dear Justin Thank you for your reply
>                                                               But For My system The Initial  Value of Box Size is (5 5 5) Not equal to Final Box Value in both X and Y dimension

So, to clarify, you're not actually doing the protein-lipid tutorial, which is 
what you said before.  If you're following the protocol, but for a different 
system, please say so.  I am not going to hazard guesses about what your system 
may or may not do; I can only speak about my own experiences with known systems.

> 6.81123   6.81123   5.00000  May Increase the  Initial Box Size ? or otherwise May I Continue the Shrinking till t Have Reached The Initial  Box Size if i Do this I Have Reached the  APL Below 62A^2

Why would you increase the initial box size?  That makes no sense at all.  Are 
the lipids in the initial configuration whole, or split across periodic 
boundaries?  Depending on the configurations of lipid tails, and whether or not 
the lipids are whole or "broken," your box size may vary.

> Hoe to Solve this Problem?  I hope on your Valuable  Suggestion ? Further Information About My System Do u Need i Will tell?

I see no evidence of a problem.  If you've got an acceptable APL, proceed.



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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