Did you have waters in the system before adding another 612? I don't know how VMD counts waters, but another way is to grep -c for SOL in the resulting gro file and divide by 3.
On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote: > Thanks for the quick reply, I have given this command to add 612 water > molecules. > genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top > > But in the solvated file, I see there are 668 water molecules. > A part of the output while adding water molecules is as follows > > Using plugin gro for structure file ala_solv.gro > Info) Using plugin gro for coordinates from file ala_solv.gro > Info) Determining bond structure from distance search ... > Info) Finished with coordinate file ala_solv.gro. > Info) Analyzing structure ... > Info) Atoms: 2026 > Info) Bonds: 1357 > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0 > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 > Info) Residues: 671 > Info) Waters: 668 > Warning) Unusual bond between residues: 1 (none) and 2 (protein) > Warning) Unusual bond between residues: 2 (protein) and 3 (none) > Info) Segments: 1 > Info) Fragments: 669 Protein: 1 Nucleic: 0 > > > On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham <[email protected]> wrote: > > On 14/08/2012 2:02 PM, tarak karmakar wrote: > >> > >> Dear All, > >> > >> Is there any way to add a specific number of water ( let say 650 > >> water) molecules while dissolving the solute in a given box ? > > > > > > Check out genbox -h > > > > Mark > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > Tarak > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
