Is the "close contact" really an issue? As soon as you start any sort of MD that will quickly adjust itself.
On Sat, 14 Mar. 2020, 7:23 pm dodia, <do...@mpip-mainz.mpg.de> wrote: > Dear gromacs users, > > I was trying a simple gmx solvate test on a water box of size 25*20*20 > angstrom, creating a water box of density 1 g/cm^3. By my calculations > the no. of water molecules in the box should by 332 (each water molecule > has a volume of (3.11 angstrom)^3). When I use the solvate command: > > gmx solvate -cs spc216 -box 2.5 2 2 -o test2.pdb -maxsol 332 > > with gromacs 5.0.7, I get 291 water molecules in the box, and the > density as 0.87 g/cm^3 > > with gromacs 2016.1, I get 295 water molecules in the box, and the > density as 0.88 g/cm^3 > > When I try using the -scale option: > > gmx solvate -cs spc216 -scale 0.40 -box 2.5 2 2 -o test.pdb -maxsol 332 > > I can get a density of 0.993 g/cm3, however when I visualize the > structure, I can notice a lot of close contact between O-O atoms (the > distance between O-O atoms becomes lower than 1.49 angstroms, the O-O > bond length). So is there any other way to fine tune the gmx solvate > command so as to generate the water box with density close to 1 g/cm^3, > without the close contact problem? > > Best Regards, > Mayank Dodia > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
