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.
Mark
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