Oh !! I got it ....it is not the -nmol but '-maxmol' thanks to both of u.......:)
On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai <p...@uab.edu> wrote: > 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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
