[gmx-users] free energy calculation and constraint distance?

[Maik Goette]

Sorry, I really didn't get, what your goal is and what, in fact, you 
really want to do.

For free energy calculations, you can
- either do Thermodynamic integration (the lambda 0/1 stuff)
- or pulling (force probe) and afterwards use Jarzynskis theorem
- or umbrella sampling together with WHAM (if I remember correctly)

Now, it's up to you, which method you favor....may also depend on your 
system/question

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


bmmothan at ucalgary.ca wrote:
> Hello Gromacs users,
> 
> I am trying to do a free energy calculation, which I have never done
> before. I have read the manual and the tutorial on the wiki but there is
> still some issues not clear to me.
> 
> I am trying to calculate free energy difference of pulling the ligand from
> a beta-sheet receptor. I understand there is a pull code with different
> options or it can be done with constraint distances.
> 
> Please correct me if my procedure is wrong: I want to constraint several
> distances between the ligand and the receptor and then  increase that
> distance to one where the ligand and receptor are completely separated.
> For that, I would have to modify my topology where i define [ constraints
> ] for the distances i want to constrain between the ligand and the
> receptor and input the bond length for state A(lamda=0) and state B
> (lamda=1) for each.
> 
> will the distances defined move the whole ligand away from the receptor?
> since am only defining several distances between ligand and receptor only.
> 
> or is it recommended to use the pull code?
> 
> Any directions is appreciated.
> 
> Belquis
> 
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