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 <tsje...@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.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 > -- Cordiali saluti, Dr.Oteri Francesco -- 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
