[gmx-users] energy minimization of a charged system in vacuum

Matthew Chan mchan3 at connect.carleton.ca
Fri Jan 28 23:57:16 CET 2011


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

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.

Thanks in advance for your replies,


Matthew Chan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110128/ce8b9047/attachment.html>

More information about the gromacs.org_gmx-users mailing list