Because you are quite greedy with parameters, one can just rougly assume
that,e.g. your distance restraints are too short and therefore just kind
of bend your ligand. Therefore it seems to find an energy minimum in
modifiying some internal degrees of freedom to your restraint potential.
Maybe you have to apply simply more distance restraints along the whole
ligand. Maybe you should stick to methods like TI or pulling, which are
implemented and heavily used within GROMACS...
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/
[EMAIL PROTECTED] wrote:
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.
Belquis
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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