[gmx-users] Re: question about free energy. Gromacs user

bmmothan at ucalgary.ca bmmothan at ucalgary.ca
Sat Aug 11 00:21:47 CEST 2007

Thank you David and Arneh for the comments.

I just have a couple of things i want to clarify about the constrain
distances i used.  The distance I used to pull the ligand and receptor
apart was a non-bonded distance between the amide nitrogen of the ligand
and the oxygen carbonyl of the receptor (on both ends).  looking at the
slowgrowth results of my 5 ns, the distances i specifed increased from
lambda 0 to 1, however, I didnt get separation as I wanted it since the
ends just separated and the middle interaction of the ligand-receptor
stayed intact. nothing unusal happened to the ligand or receptor.
I dont think my method altered the internal degrees of freedom of the
ligand. Can you please clarify this issue for me.

I used constraint=all-bonds in my mdp file.

Again, thanks you both for the comments.


>> Maybe it should be obvious, but (a) why are you constraining two
>> distances, and (b) are you sure your constraints aren't going to muck
>> with the internal degrees of freedom for the ligand? I would think one
>> would like to pull the ligand out of the receptor along some
>> particular direction, but without doing anything to alter its internal
>> degrees of freedom, or there would be a free energy associated with
>> changing its internal degrees of freedom that you wouldn't capture in
>> the PMF calculation.
> I agree with David's comments here.  Check out the 'Special Topic'
> section
> of the GMX manual.   you can either do a pulling simulation or umbrella
> sampling (where the position and constrain the ligand on some rxn
> coordinate, in several simulation).  The output of such simulatsions is a
> *.pdo file, which you can then run g_wham on to obtain a PMF.
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