On Sat, Jul 07, 2018, Meng Wu wrote:
>
> I am going to get the energy file during the MD process with Amber16
> just like the .edr file in gromacs, and I have learned that the '-e
> mden' of sander maybe it's want I want. But when I tried "pmemd.cuda
> -O -i -p -o -r -x -e ###.mden" with the pmemd.cuda, there was no
> .mden file generated. Does this mean that pmemd.cuda does not
> support generating .mden files?
Did you set the "ntwe" variable? The default is not to write mden
files. (Be sure to read the explanation of ntwe in the manual, which
describes a reason why mden files are rarely requested.)
Most people parse the mdout file: see the mdout_analyzer.py script as an
example. The "energy" action in cpptraj can also be used to get
energies if you save the coordinates in a trajectory file.
....dac
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Received on Sat Jul 07 2018 - 16:00:02 PDT
