[gmx-users] Free energy between residues

[Steven Neumann]

On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> Dear Steven,
>
> Where are you working?

I work in UK, London. Why are you asking?


> >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.

I think I will just need a potential energy between those residues (LR
and Coulombic) and then can get the effective potential
Ueff=-kTln<e(-BU)
and then g_dist.

I want to extract parameters for coarse-grained simulation.

Steven


> 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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