[gmx-users] Doubts regarding Simulation box

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 13 08:25:50 CET 2011


The distance between the solute and the sides of the box is separate from
the cutoffs. But, you want to have them large enough to avoid
self-interaction across the PBC. So the distance has to be set larger than
half the size of the cut-off. You probably shouldn't set it lower than 1nm
though, as within that range the water molecules may still experience
effects of the protei (ordering).

For the second part of your question, please refer to the manual and the
wiki, as well as to the mailing list archives.



On Jan 13, 2011 7:59 AM, <kavya at rishi.serc.iisc.ernet.in> wrote:

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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