Just a piece of advices: you can consider equilibrate a lipids system
which is large enough for your protein. This will save you huge amount
of time on using tricks to add water later or enlarge the lipids.
The system MUST BE IN PBC BOX for the g_membed input coordinate,
otherwise your job would be failed in the following step. You can
visualize your system in VMD to double check. If it is not in the PBC
BOX, you can use editconf -box to fix this issue.
good luck.
Albert
On 07/08/2013 11:40 AM, Justin Lemkul wrote:
On 7/7/13 10:52 PM, pavithrakb wrote:
Dear Sir,
Thanks so much..
now what's the solution? Should I increase the box size?
Yes. If the protein protrudes "out" of the central image, then you
will have an unstable system due to atomic overlap as well as
violations of the minimum image convention.
Already I have centered the protein and fixed the POPE membrane size.
Can you tell me how to increase the box size? or is there any other
solution?
If you need more space in the x-y plane, use genconf to replicate the
membrane patch appropriately. If x-y is sufficient and only z is the
problem, use editconf to adjust the box size and (if desired) the
location of the membrane-protein complex and then solvate with genbox
to fill the newly introduced void.
-Justin
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