[gmx-users] Directional calculation Sg and Potential

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 19 23:34:01 CEST 2010

On 20/04/2010 1:16 AM, Paymon Pirzadeh wrote:
> Hello,
> This is the second time I am sending this message.

That'd be because nobody had a good answer the first time...

> I have a protein which has a few Thr residues on one side of itself. I
> would like to know how should I setup mt index file and use which
> GROMACS tools to calculate potential energy and Sg of water molecules
> that only face these residues as a function of space coordinate such as
> z (not radial coordinate r), assuming I want my Thr residues be at the
> z=0 of the profile of Sg vs. z or PE vs z.

This sounds like a complex analysis that you will need to be prepared to 
do a lot of work to code yourself.

Cunning use of index groups with (for example) trjconv, g_traj, 
trjorder, mdrun -rerun and whatever tool calculates Sg will be required.


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