[gmx-users] desired no of water molecules
tarak karmakar
tarak20489 at gmail.com
Tue Aug 14 07:54:37 CEST 2012
sorry '-maxsol'
On Tue, Aug 14, 2012 at 11:24 AM, tarak karmakar <tarak20489 at gmail.com> wrote:
> 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 <pcl at 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 <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 |
>> ==================================================================
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> 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
--
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
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