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

Matt Chan 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:
>> 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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