[gmx-users] energy minimization of a charged system in vacuum
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.
> 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:
Since I have exactly the same needs (charged system in vacuum) I jump in...
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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