Hi,
I think that calculating a radial distribution function ('rdf' or
'radial' action) will be better for what you want to see. Just make
sure you adjust the density appropriately for whichever ion species
you're calculating it for (you want it in molecules/Ang^3).
Try something like 'radial out K.rdf.dat :K+ :614 density <density arg>'
You could also use 'grid' or 'volmap' actions to visualize the ion
density around the cofactor.
-Dan
On Thu, Nov 25, 2021 at 4:28 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Dear All,
> I want to understand how ions (Na, K and Cl) are distributed around a
> ligand during the MD simulation and if there are differences between two
> simulations.
> I have used the contacts command in cpptraj (like the following) which
> gives me the min and max distances in each frame between the ions and
> residue 614.
> My question is how to get more of a statistical analysis of the
> distribution of ions around the cofactor. Can I use the closest command to
> get what I want here? if yes, what options I should use?
>
> Please do give your valuable suggestions.
>
>
> nativecontacts name cofac-K :614&!.H= :K+ byresidue out cofac-Kcontacts.dat
> mindist maxdist distance 10.0 first map mapout cofac-Kresmap.gnu contactpdb
> cofac-Kcontactmap.p
> db series seriesout cofac-Knativecontacts.dat writecontacts
> cofac-Kwritecontacts.dat
>
> Thank you and best regards.
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Asst. Prof., Department of Medicinal Chemistry,
>
> National Institute of Pharmaceutical Education and Research, Guwahati
> (NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
> 781101, Assam, India
>
> Mob. No. +91-7709129400,
> Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
> https://niperguwahati.ac.in/DOC/profile/dixit.pdf
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> NCBI bibliography:
> https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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Received on Wed Dec 01 2021 - 06:00:02 PST
