[gmx-users] Doubts regarding Simulation box

kavya at rishi.serc.iisc.ernet.in kavya at rishi.serc.iisc.ernet.in
Thu Jan 13 07:07:55 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 when giving the simulation box, should i give the
value of -d as >=1.2nm?

Does this same rule apply to a cubic box also?

when I am using dodecahedron box with -d as 1.3nm, the waters
added using the command:

genbox -cp box-1-11.pdb -cs spc216 -p topol-1-11.top -o water-1-11.pdb

Water box appears cubic and goes out of the dodecahedron box used.
Why is this happening and what is the solution for this? Kindly
give some suggestions.

Thanks in advance

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