[gmx-users] desired no of water molecules
Peter C. Lai
pcl at uab.edu
Tue Aug 14 06:43:45 CEST 2012
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
> 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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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
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