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