[gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  =  5.9483964e+18
> > Maximum force     =            inf on atom 6710
> > Norm of force     =            nan
>
> How did you add these new waters? Should your system be periodic? Does
> visualising the start, progress and end of the EM trajectory shed any
> light on what is going wrong?

The waters were added using a modification of the make_hole script that is
widely used.  A member of our lab tweaked it a few years ago, and we apply it
to a number of systems.  I created a box of water large enough to solvate my
protein, and inserted the bilayer/crystal water system into it, with minimal
overlap, but enough such that a few waters were deleted from the original box.

Another note is that I have tried the minimization a couple times (with
insignificant changes to my .mdp file, as it turns out), and the infinite force
keeps changing location.  Is that maybe a clue as to what is going on?

The system does not need to be periodic.  When I took a look at velocities and
forces with g_traj (from the default output traj.trr), there were no velocities
found (probably due to the fact that I did not set gen_vel = yes), and the
forces were all 'nan.'  Is there another way to look at my trajectory output
that might be of more use?  (Again, still new to Gromacs and very
overwhelmed/impressed by the myriad function it can perform.)

Thanks in advance for any more information you may be able to provide.

-Justin

Justin A. Lemkul
Biochemistry
Alpha Chi Sigma, AI '04
Virginia Tech