Sorry, the input file is here.
2013/5/6 Deák Robert <kokumetto.gmail.com>
> 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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- application/octet-stream attachment: prod.in
Received on Mon May 06 2013 - 06:30:03 PDT
