On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask in
separate emails. The first is about running EM on a charged protein in
vacuum.
I'm presently walking through some of the tutorials and trying to
simplify them for my purposes. One is the energy minimization of the
1AKI lysozyme protein. I would like to minimize this protein in vacuum
instead of solution as the tutorial demonstrates. Since the genion
program replaces water molecules with ions to balance the charge of
the system and there's no water, I'm having trouble running the
simulation with a neutral system.
My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing list, I have
only been able to determine that running a charged system in solution
makes no sense biologically.
Some threads elsewhere cover these issues:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
http://archive.ambermd.org/200712/0223.html
Mark
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