[gmx-users] parameter on Energy Minimization

Mark Abraham mark.abraham at anu.edu.au
Tue Mar 11 23:58:21 CET 2008

> Hi,
> I used a script given below for energy minimization of  a native
> protein-protein complex 1akj.
> I removed HETATMs and water molecules from the structure, and the
> minimized
> structure  (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.
> Then I used rasmol to check the result.  The ligand is ran away from
> receptor.
>  rasmol 1akj_oplsaa.minim_traj.pdb

As Justin said, you might well be observing a PBC artefact. Having not
turned off PBC in your .mdp file, or used editconf to change the size of
the box that pdb2gmx chooses, then your EM is probably using defaults that
you'd rather not use.

> Then I tried the larger epsilon_r           =  800000.0, and got very
> similar result. I mean that for two substantially different values of the
> epsilon_r minimization gives absolutely the same final positions of the
> ligand.

Being good scientists, we deduce that the approximate location of the
local energy minimum from this starting point is not dependent on the
dielectic of the medium. :-)

> I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,
> G45a3, G53a5, G53a6,  gmx, oplsaa.
> I also got similar result.



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