[gmx-users] Setup Box Size

[Nuno R. L. Ferreira]

Hi Dr. Kerrigan

I'm more aware now about the box size problems.
I agree that one important aspect is the relative flexibility of the solute
to be studied.
Talked to someone that is doing protein unfolding by MD in my group (but
with another soft pack). This is a case where it's very difficult to set a
priori, a box size large enough to accomodate the "open" states of the
protein and a secure shell of water around those protein unfolding states,
during the full MD course.

BTW, what do you (all gmx users) think we should do if at certain point of
the simulation the box becomes "too short" to have a protein not seeing its
periodic images? Stop the run, search a frame to begin a new md where
there's not yet pbc problems, perhaps center the protein in the box, and
continue from here?  Is it possible to increase the box size at certain
frame (adding more solvent), without having big energetic problems at the
interface between the old box edge and the new solvent layer, nor affecting
the protein stability?

Thank you by your pedagogic answer, and tutorials. Keep on.

Kind regards,
NUno


######################################
Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
########################################