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

[Mark Abraham]

On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri <francesco.oteri at gmail.com
> wrote:

> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>

Don't change things until you know *why* they don't work. That means
visualizing the results of the recommended workflow until you see a problem
emerge (which I think is in your starting protein configuration, if the
standard procedure also gave problems).

Why did you decide to double the margin to 0.8nm? You would create an
unphysical void, so numerical instability seems pretty likely. (But I think
you have a more serious problem as well.)

Even if this change was needed, you may as well do both clash-avoidance
procedures, in case there are things going on that you haven't thought of.

Looking carefully at the configurations, I found that the water molecule
> originating the error is exactly superimposed to an other molecule so I
> simply deleted it and the same error is reported for an other water
> molecule.
>
> Although I could scan all the pdb to detect all the superimposed water
> molecules, I believed genbox checked for this. Of course the original box
> does't contain superimposed molecules.
>

Shrug. You need to look at your intermediate structure files and find where
the problem first appears.

Mark


>
>
> Francesco
>
>
> 2012/12/10 Justin Lemkul <jalemkul at vt.edu>
>
> >
> >
> > 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
> >
> > --
> > ==============================**==========
> >
> > 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<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> > --
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>
> --
> Cordiali saluti, Dr.Oteri Francesco
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