[gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

> 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.

Apologies for the confusing description...I think I figured that problem out,
however.  I fixed the box dimensions in the .gro file and it is now
appropriately centered.

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

The system is now centered, using this command, however, I am still getting the
same output - infinite force on a solvent atom, and an exceptionally high
potential:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  5.9484382e+18
Maximum force     =            inf on atom 6417
Norm of force     =            nan

I also tried running a position-restrained MD (just to see if it might give me
something different), holding the DPPC bilayer fixed and allowing the solvent
to move, but I was again frustrated to see:

Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.

In the MD, I am applying PBC.  I am wondering if this output is a result of a
poorly minimized starting structure, or if these errors are in any way related?

Thanks for any thoughts,
Justin