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

Justin Lemkul jalemkul at vt.edu
Mon Dec 10 23:18:22 CET 2012

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


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