Dear Amber users,
Recently I have done a test.
The system is a single ARG solvated in a truncated octahedron water box,
with a 9A TIP3P water buffer aroud the ARG.
A have minimized, heated to 340 K and equlibrated the system, like in the
Tutotial 1, and the production MD (the input file prod.in is attached) went
well.
Now comes the test.
I have multiplied all the masses in the system with 4 (using parmed). The
new dt and taup are doubled and gamma_ln is the half of the earlier one.
Theoretically the extracted data for the diffusion of the ARG and the
increased mass ARG (mass x 4) are the same.
While for the first system everything seems OK, following the center of
mass of ARG (mass x 4) the y coordinate of the molecule is almost
continously increasing, while the x and z shows diffusion like paths.
Can somebody explain me why is happening this, or this is a bug?
Regards,
Robert
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Received on Mon May 06 2013 - 06:30:02 PDT
