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

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 11 00:06:21 CET 2012

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.


>> 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>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

More information about the gromacs.org_gmx-users mailing list