For Justin, I need this water for one simple reason: less then 20nm doesn't work....As I said before
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. > > > 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 > -- 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