[gmx-users] About Box Vector
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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