[gmx-users] desired no of water molecules
tarak karmakar
tarak20489 at gmail.com
Tue Aug 14 07:54:17 CEST 2012
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 |
> ==================================================================
>
> --
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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
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