On Fri, Feb 23, 2018, Vikram Dalal wrote:
>
> I want to know that on what basis we have to select the specific type of a
> box for a particular protein during molecular dynamics in AMBER ?
If you are doing a "solution" simulation (single protein in water), you have
two main choices:
a. what shape of box to use: rectangular (using solvateBox) or truncated
octahedron (using solvateOct). The octahedron is closer to a sphere (so
that the orientation of the protein matters less), and places more
water near the protein (for a given number of water molecules, assuming
that the protein itself is roughly spherical.)
b. How many water molecules to include. As GPUs become more powerful,
people have been migrating to having bigger water shells, often in
the range of 15 Ang. Others may want to chime in here with specific
anecdotes, but you should be wary of having too small a shell. I
personally would no longer try shells less than 12 Ang, but that opinion
is *not* based on any systematic study.
...hope this helps....dac
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Received on Fri Feb 23 2018 - 05:30:02 PST
