[gmx-users] Energy Minimization with Lipid Bilayer

[Mark Abraham]

Justin Lemkul wrote:

> 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?

Hmmm in order that we can see what your .gro file is doing, can you 
please post the results of

head -n 10 conf.gro
tail -n 10 conf.gro
wc -l conf.gro

Mark