[gmx-users] Energy Minimization with Lipid Bilayer

[Mark Abraham]

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?

I'm confused about what you've reported doing. If the box is 
rectilinear, then it should be a straightforward case of adding the 
increase caused by the slab to one of the dimensions at the bottom of 
the .gro.

>>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?

Don't know. editconf -c and see if that works.

Mark