[gmx-users] Energy Minimization with Lipid Bilayer

[Mark Abraham]

Justin Lemkul wrote:
> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> 
> 
>>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
> 
> 
> Hopefully this will help:

Unfortunately all seems to be in order there. The second line has the 
right number of atoms for the number of lines in the file, and the box 
in the final row has the right format.

Can you mail me your .gro, .mdp and .top (and appropriate #included .itp 
files) off-list and I'll take a look?

Mark