[gmx-users] box size and neighbor list cut-off

Johnny Lu johnny.lu128 at gmail.com
Mon Aug 17 20:02:26 CEST 2015

Dear Users,


Box vector length:
      3.448, 3.448, 3.448 nm dodecahedron.
      (Box volume is 28.98 nm^3)

Diameter of tripeptide:
      1.248 nm

Volume of tripeptide:
      0.35503 nm^3 (from genbox output)

Short range Neighbor list cut-off:
      1.1 nm (set manually by rlist=1.1)

Other short range cut off (VdW and electrostatic):
      1.0 nm

According to 5.2 manual (manual-5.2-dev.pdf),
      "This means that the length of each box vector must exceed the length
of the macromolecule in the direction of that edge plus two times the
cut-off radius R_c"

Box vector length >= Diameter of peptide + 2 x cut-off
      3.448 = 1.248 + 2 x 1.1

Do I have to leave any leeway in the box size? (say, a box size of 3.5 nm)

I will run a NPT simulation (Berendsen barostat). Then continue the
simulation with a NVT simulation. And finally continue the NVT simulation
with a NVE simulation.

Last time when I ran a double precision NVE simulation, I set rlist=1.3 and
used a 4.848^3 nm^3 dodecahedron box. The energy conservation was good. If
I use a 1.1nm rlist, will I get an energy conservation that is nearly as
good as the rlist = 1.3nm simulation?

Thank you again.

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