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

ms devicerandom at gmail.com
Sun Jan 30 16:02:51 CET 2011

On 29/01/11 05:08, Matt Chan wrote:
> Perfect. This is great reading.
> Thanks for the pointers Mark.
> Matt
> 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

Since I have exactly the same needs (charged system in vacuum) I jump in...

In http://www.gromacs.org/Documentation/Errors
it says:

Note for PME users: It is possible to use a uniform neutralizing 
background charge in PME to compensate for a system with a net 
background charge. There is probably nothing wrong with this in 
principle, because the uniform charge will not perturb the dynamics.

 From the reading above, it seems that namd/amber implementations 
already *implicitly* use this kind of compensation by ignoring terms in 
the summation. Is it the same for GROMACS?


Massimo Sandal, Ph.D.

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