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

[Tsjerk Wassenaar]

Hi,

Visualization is the key. If you check the structure right after genbox,
you should be able to notice something odd. Apparently genbox has a problem
with martini water, which probably means there is a problem with monoatomic
solvents. The problem has been noted before, b ut I'm a bit too lazy now to
check whether it was here or on the martini forum. Using a small box with a
single water molecule for filling will solve the problem.

Cheers,

Tsjerk


On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 12/10/12 5:45 PM, francesco oteri wrote:
> >
> >> For Justin,
> >> I need this water for one simple reason: less then 20nm doesn't
> work....As
> >> I said before
> >>
> >>
> > It seems you have identified the source of the problem, and it is
> > independent of box size.  I questioned the box size because it seemed
> > rather random and you had not shown any data for box sizes less than 19
> nm,
> > so I was curious how you arrived at the need for 20 nm, more than double
> > the size of your solute.
> >
> > It would be interesting to see if you could identify a minimum box size
> > that does not require large numbers of solvent configurations to be
> stacked
> > within the unit cell.  The only reason I could see for what you're
> > reporting is if neighboring solvent blocks somehow get crossed to produce
> > overlap when they should simply be next to one another.  The larger the
> > box, the greater the probability that this happens.
>
>
> Yeah, that's probably it. The water box has many waters with x coordinates
> down at 0.000 and near 10.901, with an x size of 10.902. So different box
> sizes will randomly introduce unstable water configurations according to
> whether stuff is too close. This water box is probably not suited to the
> purpose - its "box size" might not include the half VDW radii outside the
> water coordinates needed to pack stably.
>
> Mark
>
>
> >
> >
> >> 2012/12/10 francesco oteri <francesco.oteri at gmail.com>
> >>
> >>  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.
> >>>
> >>> 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.
> >>>
> >>>
> >>>
> > It is highly unusual for genbox to produce overlapping waters, but per
> the
> > help description, only solute-solvent overlaps are checked, not
> > solvent-solvent, which would likely require enormous amounts of memory
> (and
> > genbox already has memory issues).
> >
> > -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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada