[gmx-users] energy minimization of a charged system in vacuum
talcite at gmail.com
Sat Jan 29 06:08:46 CET 2011
Perfect. This is great reading.
Thanks for the pointers Mark.
On 01/28/2011 06:50 PM, Mark Abraham wrote:
> On 29/01/2011 9:57 AM, Matthew Chan wrote:
>> 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:
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