[gmx-users] Energy Minimization with Lipid Bilayer

Steffen Haerterich haerterich at apollo1.pharmazie.uni-erlangen.de
Tue Nov 21 08:30:32 CET 2006


As you mentioned before you are not using PBC. However, if the membrane 
in the box was equilibrated using PBC then it might be that some residues 
are "cut in a half". So perhaps take a look at your Lipids and make sure that 
all parts of a phospholipid molecule are on the same side of the box.
Just a thought, might be pointless.


On 20 Nov 2006 at 18:36, Justin Lemkul wrote:

> > 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
> Justin A. Lemkul
> Undergraduate Researcher
> Department of Biochemistry
> Viriginia Tech
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