[gmx-users] Error with MARTINI depending by the box size

[Justin Lemkul]

On 12/10/12 5:15 PM, francesco oteri wrote:
> Actually, since I copied and pasted the mail, there is an imprecision. When
> I use 20nm as box side lenght I don't get
> any error, everything goes fine.
>
> I actually tested different size between 19 and 20 nm and I found that the
> minimum size to avoid the error is 19.5nm.
> My system has an average size and, as stated by vmd, it size are
> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
> So a box of 20nm, as well as 19nm, is large enough to accomodate the
> protein.
>

Those box sizes are vast overkill.  Any reason why you need so much extra water?

> Moreover, since I remove the water around the protein (that is already
> stabie because of the in vacuo minimization), the problem has to be in the
> bulk water!
>

As I said before, you should be able to identify the source of the problem by 
simple visualization based on what mdrun has told you.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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