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
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