[gmx-users] desired no of water molecules
Peter C. Lai
pcl at uab.edu
Tue Aug 14 07:05:58 CEST 2012
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 <pcl at 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.Abraham at 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
> >> > --
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> >>
> >>
> >> Tarak
> >> --
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> > --
> > ==================================================================
> > Peter C. Lai | University of Alabama-Birmingham
> > Programmer/Analyst | KAUL 752A
> > Genetics, Div. of Research | 705 South 20th Street
> > pcl at uab.edu | Birmingham AL 35294-4461
> > (205) 690-0808 |
> > ==================================================================
> >
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>
> Tarak
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--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
==================================================================
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