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a-anik / cavity-volumes-pbc

Voronoi-based calculation of cavities inside molecular dynamics models with periodic boundary conditions
GNU General Public License v3.0
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after cmake .. step no binary file was found #1

Closed deleep225 closed 4 years ago

a-anik commented 4 years ago

Thank you for your feedback! You are right. Binary file should be created after the final make command, which I missed out in my quick steps guide.

deleep225 commented 4 years ago

thank you.

On Tue, Nov 26, 2019 at 8:31 PM Alexey Anikeenko notifications@github.com wrote:

Closed #1 https://github.com/a-anik/cavity-volumes-pbc/issues/1.

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deleep225 commented 4 years ago

respected sir, I am using vnp software to calculate the void radii. (windows) I have provided the coordinates and the radii of atoms of ionic liquid. (all atom)

I considered the van der Waals radius of atoms. I am getting negative values of radii. Is there anything wrong in my procedure. Thank you for your time.

On Thu, Nov 28, 2019 at 2:01 PM deleep reddy deleep225@gmail.com wrote:

thank you.

On Tue, Nov 26, 2019 at 8:31 PM Alexey Anikeenko notifications@github.com wrote:

Closed #1 https://github.com/a-anik/cavity-volumes-pbc/issues/1.

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a-anik commented 4 years ago

It totally makes sense. What you get is actually a weight in additively-weighted Voronoi diagram. It can be negative. In that case it means that the "inscribed" sphere for the tetrahedron is covered by its atoms and touches them from the inside. No void space is contained in such Delaunay simplexes. Only positive radii correspond to real empty inscribed spheres.

deleep225 commented 4 years ago

Thanks for your kind reply. In that case, I have calculated the distribution for only positive values.

The graph I have attached.

My system is pyrrolidinium TFSI ionic liquid.

I am trying to calculate the distribution of interstitial spheres similar to "Comparing the void space and long-range structure of an ionic liquid with a neutral mixture of similar sized molecules"

Kindly can you comment on my result as I am doing it first time. I am very grateful for your help.

On Thu, Nov 28, 2019 at 5:00 PM Alexey Anikeenko notifications@github.com wrote:

It totally makes sense. What you get is actually a weight in additively-weighted Voronoi diagram. It can be negative. In that case it means that the "inscribed" sphere for the tetrahedron is covered by its atoms and touches them from the inside. No void space is contained in such Delaunay simplexes. Only positive radii correspond to real empty inscribed spheres.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/a-anik/cavity-volumes-pbc/issues/1?email_source=notifications&email_token=AKLUWCSEDBK2Z7JHGQPO3YLQV6TU5A5CNFSM4JRTM6EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMKFFI#issuecomment-559456917, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKLUWCSBREUR7BBPFM5QRODQV6TU5ANCNFSM4JRTM6EA .