[gmx-users] Energy Minimization with Lipid Bilayer

Justin Lemkul jalemkul at vt.edu
Tue Nov 21 00:36:46 CET 2006

> This sounds like you are adding a slab onto one end of the box, rather
> than replacing part of the box... did you adjust the box dimensions
> accordingly? (They're on the bottom line of a .gro file.) If so, gromacs
> might be getting confused about the positions of atoms outside the
> box... but this is me clutching at straws.

That's exactly what I'm doing.  I adjusted the box size by doing a dummy
editconf command (telling it to rotate 0 degrees about all axes) to generate
the new box dimensions.  I manually fixed these at the bottom of my system's
.gro file.  Is that an appropriate procedure?

> Use something like VMD (or the GROMACS built-in ngmx) to view the
> positions over the "trajectory" (EM provides a series of coordinate sets
> according to nstxout, not a true trajectory) - either the first step or
> final coordinates are probably enough to point out what is wrong.

This may have given me a clue.  Using ngmx (a handy little tool), I found that
my system was positioned in the lower left-hand corner of the box shown on the
screen.  I'm wondering if this is somehow a consequence of how I approached
defining the box size.  Could this be part of my problem?

> Viewing forces or velocities is a great way to start suffering from
> epilepsy.

Agreed; luckily I was able to generate a .pdb file with the forces in it, and
that's how I saw all the 'nan'!

Any new ideas?

Always grateful,

Justin A. Lemkul
Undergraduate Researcher
Department of Biochemistry
Viriginia Tech

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