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