[gmx-users] Analysis

[Mark Abraham]

Hi,

On Thu, Jun 1, 2017 at 3:35 PM RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> I have few doubts in MD analysis.
>
> *How to calculate the deviation angle between two helix of a protein? (for
> every ns) or in other words how can I know whether the two helices
> (consecutive)
>  have moved apart during simulation?
>

Various of the analysis tools may be helpful here. Start at
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#commands-by-topic


> *In saltbridge analysis how can I eliminate CL and NA ions? (Before the
> analysis)
>

Probably through use of suitable index groups, which you probably learned
about in tutorials or have seen in the documentation.

Mark


> PS:- Its Protein-Ligand complex simulated for  100ns.
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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