[gmx-users] desired no of water molecules

[Peter C. Lai]

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
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