[gmx-users] box size and pbc

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 10 11:00:46 CET 2006

Hi Guys,

First off, a small correction. The default option of editconf is not a cubic
box, but a rectangular one. The use of counterions in the case of oppositely
charged ends could be a solution, but I would advice to use counterions +
physiological concentration of NaCl (0.1536M or so) to assure that there's a
proper ionic strength and there's always a proper counterion around; just
like in real life. However, it is still better to choose the box to have
such a size that the protein/peptide will fit whatever happens during the
run. If that means unfolding, the box should be large enough to contain the
stretched molecule with extra space to keep it from direct interaction over
the boundary. In addition, if the solute is free to rotate, the size should
be large enough in all directions. A good reason to use a rhombic
dodecahedron. It would be possible to use rotational constraints if the
conformational changes during the simulations aren't too dramatic.
Otherwise, you've got bad luck.



Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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