hmm. What happens if you try -maxsol instead of -nmol? On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote: > This is the ala.gro (alanine dipeptide) file which does not contain > any water (SOL) a priori. > > Grunge ROck MAChoS > 22 > 1ACE HH31 1 1.267 1.058 1.673 > 1ACE CH3 2 1.364 1.086 1.631 > 1ACE HH32 3 1.422 0.996 1.607 > 1ACE HH33 4 1.416 1.148 1.705 > 1ACE C 5 1.348 1.183 1.515 > 1ACE O 6 1.381 1.152 1.401 > 2ALA N 7 1.301 1.303 1.549 > 2ALA H 8 1.284 1.324 1.646 > 2ALA CA 9 1.290 1.409 1.450 > 2ALA HA 10 1.374 1.399 1.381 > 2ALA CB 11 1.160 1.402 1.371 > 2ALA HB1 12 1.131 1.299 1.351 > 2ALA HB2 13 1.086 1.455 1.431 > 2ALA HB3 14 1.166 1.447 1.272 > 2ALA C 15 1.301 1.548 1.510 > 2ALA O 16 1.277 1.567 1.629 > 3NME N 17 1.337 1.646 1.426 > 3NME H 18 1.356 1.619 1.330 > 3NME CH3 19 1.344 1.784 1.469 > 3NME HH31 20 1.408 1.835 1.398 > 3NME HH32 21 1.250 1.838 1.469 > 3NME HH33 22 1.394 1.797 1.565 > 0.33600 0.84200 0.43300 > > > If I grep 'SOL' ala_solv.gro , then it is showing > > 4SOL OW 23 0.569 1.275 1.165 > 4SOL HW1 24 0.476 1.268 1.128 > 4SOL HW2 25 0.580 1.364 1.209 > ...................................... > ................................... > 668SOL OW 2015 0.755 0.751 0.211 > 668SOL HW1 2016 0.785 0.679 0.149 > 668SOL HW2 2017 0.716 0.711 0.294 > 669SOL OW 2018 2.632 0.122 2.163 > 669SOL HW1 2019 2.586 0.035 2.180 > 669SOL HW2 2020 2.723 0.119 2.204 > 670SOL OW 2021 0.144 1.914 2.030 > 670SOL HW1 2022 0.179 1.873 1.946 > 670SOL HW2 2023 0.054 1.876 2.050 > 671SOL OW 2024 1.901 2.939 2.162 > 671SOL HW1 2025 2.000 2.928 2.153 > 671SOL HW2 2026 1.861 2.853 2.194 > > so certainly it does contain 668 water molecules. > Thanks, > > On Tue, Aug 14, 2012 at 10:13 AM, Peter C. Lai <p...@uab.edu> wrote: > > 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 <mark.abra...@anu.edu.au> > >> 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 gmx-users@gromacs.org > >> > 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 gmx-users-requ...@gromacs.org. > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > >> > >> Tarak > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> 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 gmx-users-requ...@gromacs.org. > >> * 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 > > p...@uab.edu | Birmingham AL 35294-4461 > > (205) 690-0808 | > > ================================================================== > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > Tarak > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * 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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
