From: Yingzhe Liu (lyz894_at_mail.nankai.edu.cn)
Date: Wed Jun 22 2011 - 02:53:56 CDT
I want to simulate the adsorption of protein on the substrate, namely mica.
The protein is neutral and the surface of mica carried a charge density of
¦Ò = -0.021 e/A*^2 .
If I add counter ions randomly using the autoionize plugin of VMD to make
the whole aqueous system neutral, the counter ions would adsorb on the mica
surface quickly due to the strong electrostatic attraction. However, the
is not electronegative any more, which is inconsistent with the experiments.
If I do not add counter ions, the molecular system is not neutral, which
required by PME algorithm.
In addition, to eliminate the effect of mica images on protein, can PBC
applied to two directions in NAMD?
Thanks in advance.
-- Yingzhe Liu Ph.D. Student of Analytical Chemistry Chemistry Department, Nankai University Tianjin, P.R.China, 30071 Tel: +86-022-23509425 Web: http://chinfo.nankai.edu.cn/
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