Justin Lemkul wrote:
Quoting Mark Abraham <[EMAIL PROTECTED]>:
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
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