[gmx-users] genion - why shall we neutralize the charges?

Yang Ye leafyoung at yahoo.com
Mon Jun 11 20:04:43 CEST 2007


First, our simulation system in physical world are mostly neutralized instead of carrying charges. Second, there is requirement for PME for electrostatic calculations. Neutralization is a not a must in 3.3.1 Gromacs; a background charge will complement for the charges that system carries, but it is always good to put explicit ions. Besides neutralization of charge, it is also reminded to keep total charge at an integer or very close to an integer (due to floating number representation in computer). 

A personal note to you: please use regular and scientific words for this mailing list. It is not easy to get to know what you are asking.

Yang Ye

----- Original Message ----
From: Elias santos <silvasantosster at gmail.com>
To: gmx-users <gmx-users at gromacs.org>
Sent: Tuesday, June 12, 2007 1:34:39 AM
Subject: [gmx-users] genion


I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. 

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