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.abra...@gmail.com>wrote: > On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul <jalem...@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.ot...@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@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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
