[gmx-users] desired no of water molecules
Mark.Abraham at anu.edu.au
Tue Aug 14 07:05:47 CEST 2012
On 14/08/2012 2:37 PM, 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
That's not how to use -nmol, nor is it the right option to solve your
problem. There's an option that sets a maximum number of solvent
molecules. Read about it and use it :-) If your volume is too large for
that number, you'll have issues later.
> But in the solvated file, I see there are 668 water molecules.
Yes, genbox reported how many it added. No need to use VMD to count them
if you read the output of the tool you used.
> 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
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