[gmx-users] Free energy between residues

[lloyd riggs]

Dear Steven,

Where are you working?

>From my experience the g_energy  -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet.  if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me.

Sincerely,

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Thu, 28 Jun 2012 09:28:09 +0100
> Von: Steven Neumann <s.neumann08 at gmail.com>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: [gmx-users] Free energy between residues

> Dear Gmx Users,
> 
> I want to obtain the free energy difference between the pair of
> residues in my protein chain with respect to thheir distance. Would
> combinbation:
> 
> 1) g_dist - distances between two groups during the simulation time
> 
> 2) g_energy -fee (DelatG - with energy groups I am interested in
> stated in mdp file)
> 
> give me those values?
> 
> Or I should use PMF - umbrella sampling with the bias (harmonic)
> potential introduced?
> 
> Thank you,
> 
> Steven
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