[gmx-users] Doubts regarding Simulation box

Kavyashree M hmkvsri at gmail.com
Thu Jan 13 09:49:16 CET 2011

Dear Gromacs users,

    I am new to gromacs. I want to simulate a system
(protein) with a dodecahedron box in order to minimize
the time.

rlist = rcolumb = 1.2nm;              (PME)
rvdw = 1.1nm; rvdw_switch = 0   (using vdwtype = switch)

so while setting the simulation box, should i give the
value of -d as >=1.2nm?

Does this same rule apply to a cubic box also? ie.,
irrespective of the box I use whether dodecahedron, cubic or
octahedron, according to the cutoff (max (rlist, rvdw, rcoloumb))
I have to use -d as 1.2nm, or higher?

Kindly anyone clarify my doubts

Thanks in advance.
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