[gmx-users] Energy Minimization with Lipid Bilayer

[Steffen Haerterich]

Hallo!

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.

Yours,
Steffen


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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