[gmx-users] Regarding the code for HB auto-correlation function code

[David van der Spoel]

Den 2018-06-15 kl. 07:39, skrev Dilip.H.N:
> Sir,
> I have done the simulation of amino-acid+water+cosolvents in GROMACS and 
> now i want to calculate the HB auto-correlation functions.In GROMACS 
> there is only intermittent HB and not Continuous HB. And hence i am 
> trying with MDAnalysis which is a python module but in vain.
> 
> I have read your paper entitled "Thermodynamics of Hydrogen Bonding in 
> Hydrophilic and Hydrophobic Media" and is really a good paper sir.
> 
> I want to know how did how to calculate the HB Auto-correlation 
> functions there.
> Which programming language did you use for the code, sir? If possible 
> can u share the code or help me here sir..
> 
> Any suggestions are highly appreciated sir.
> 
> Thank you.
> 

You can do the continuous version with gmx hbond -life as well, but as 
we argue in the paper, the non-continuous version is more meaningful, 
since the continuous version depends on the frequency of saving the 
trajectory.

Please ask further questions on the gmx-users mailing list.

> ---
> With Best Regards,
> 
> Dilip.H.N
> PhD Student.
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> 06/15/18, 11:09:42 AM 	
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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