[gmx-users] Energy Minimization with Lipid Bilayer

Justin Lemkul jalemkul at vt.edu
Mon Nov 20 04:31:50 CET 2006

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

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