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
