[gmx-users] desired no of water molecules

[tarak karmakar]

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