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

[francesco oteri]

Tanks to all for your advices,
I am going to check all the different aspect you suggested and I will
report the results as soon as possible.

Francesco


2012/12/11 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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
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-- 
Cordiali saluti, Dr.Oteri Francesco