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. Francesco 2012/12/10 Justin Lemkul <jalem...@vt.edu> > > > On 12/10/12 5:15 PM, francesco oteri wrote: > >> Actually, since I copied and pasted the mail, there is an imprecision. >> When >> I use 20nm as box side lenght I don't get >> any error, everything goes fine. >> >> I actually tested different size between 19 and 20 nm and I found that the >> minimum size to avoid the error is 19.5nm. >> My system has an average size and, as stated by vmd, it size are >> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986 >> So a box of 20nm, as well as 19nm, is large enough to accomodate the >> protein. >> >> > Those box sizes are vast overkill. Any reason why you need so much extra > water? > > > Moreover, since I remove the water around the protein (that is already >> stabie because of the in vacuo minimization), the problem has to be in the >> bulk water! >> >> > As I said before, you should be able to identify the source of the problem > by simple visualization based on what mdrun has told you. > > > -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> > -- 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