[gmx-users] Energy Minimization with Lipid Bilayer
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
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?
Justin A. Lemkul
Department of Biochemistry
More information about the gromacs.org_gmx-users