[gmx-users] Simulation of charged systems (2)

Felipe Pineda, PhD luis.pinedadecastro at lnu.se
Tue Nov 6 09:27:34 CET 2012


thanks to Justin for the pointer to the list archive I searched before 
with "net charge", but without getting useful results. For the sake of 
clarity, I am not referring to the "neutralizing plasma" or neutralizing 
background charge used implicitly with PME, but to an additional 
net-charge correction implemented for example in CHARMM to avoid, at 
least partly, the artifacts produced by that neutralizing background 
charge in net-charged systems, which are sometimes unavoidable (s., eg., 
Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy 
artifacts in charged periodic systems via net charge corrections to the 
ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84. 


On 11/05/2012 02:27 PM, Justin Lemkul wrote:
> On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote:
>> Hi again!
>> many thanks to Xavier for his response, the only one I got so far ... I had the
>> same impression, but I'm seeking for theoretically/technically more funded
>> statements. My impression is also that there are different kind of "equations"
>> depending of the treatment of long-range electrostatic interactions.
>> My concrete question is now: are net charge corrections to the Ewald potential
>> implemented in Gromacs?
> http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html
> Searching the list archive for "neutralizing background charge" turns up a large
> number of results.  This is a fairly common question, and there are many replies
> with varying degrees of detail.
> -Justin

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