[AMBER] Force Trajectory Output ABMD

From: Jonathon Ferrell <jonathon.ferrell5156.gmail.com>
Date: Mon, 6 Jul 2020 12:56:24 -0400

Hello All,

If the answer to this first question is no, the rest of the email can
be discarded. Do the forces written out by ntwf=-1 in an ABMD
simulation using pmemd.cuda include the bias forces (resulting from
the added bias energy)?

Else, I am having trouble getting the outputs of esander, sander with
imin=5 to agree with the forces output by a normal MD simulation (also
pmemd.cuda). I am using the amber19ff and opc water, I know when using
esander it raises errors like "Warning: Amber topology flag
'CMAP_COUNT' is unrecognized and will be skipped." I also know of the
off by one frame error that is common from comparing the two
simulations but even checking 5 sequential frames, none of the forces
(either esander or imin=5) match with the output forces from a normal
MD simulation, and at a difference much larger than the expected error
from the paper I read on the pmemd.cuda implementation. They do
however agree with each other. Is there something I am missing in this
or otherwise obviously getting wrong?


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Received on Mon Jul 06 2020 - 10:00:03 PDT
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