[gmx-users] Regarding finding orientation of angles of solvent with desired atom

[Dilip H N]

Hello,

I have simulated amino acid (eg., glycine) with water solvent mixture in
gromacs..
my question is ..
1] How can i find out the solvent orientation (angle made) ie.,angle made
by water (HOH) with respect to alpha carbon of amino acid (eg.,
glycine)...??
2] I have tried with gmx sorient command ..it gives me five outputs..sori,
snor, sord, scum, scount. With sori (it gives from solvent orientation -
cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
theta 0 to 1) , but with what respect is it giving i am not able to
understand...
3] I wanted to calculate the angle formed between water (HOH) and alpha
carbon of glycine. but if it consider the .gro file, i can calculate the
angle for only the last frame... but i want to calculate the angle for the
full frame (tpr/trr). How can i do it ...Can anybody kindly help me
regarding this..

Thank you...



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On Mon, Apr 24, 2017 at 1:22 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Hello,
>
> I have simulated amino acid (eg., glycine) with water solvent mixture in
> gromacs..
> my question is ..
> 1] How can i find out the solvent orientation (angle made) ie.,angle made
> by water (HOH) with respect to alpha carbon of amino acid (eg.,
> glycine)...??
> 2] I have tried with gmx sorient command ..it gives me five outputs..sori,
> snor, sord, scum, scount. With sori (it gives from solvent orientation -
> cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos
> theta 0 to 1) , but with what respect is it giving i am not able to
> understand...ie theta 1 and theta 2
> 3] I wanted to calculate the angle formed between water (HOH) and alpha
> carbon of glycine. but if it consider the .gro file, i can calculate the
> angle for only the last frame... but i want to calculate the angle for the
> full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding
> this..
> Since i am referring one of ur research paper - [Glycine in aqueous
> solution: solvation shells, interfacial water, and vibrational spectroscopy
> from ab initio molecular dynamics]. and in other paper - [MONTE CARLO
> SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they
> have calculated the cos theta distribution functions...so i wanted to
> calculate ..
>
> Thank you sir...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student