How to simulate a charged surface

From: Yingzhe Liu (yingzhe.cn_at_gmail.com)
Date: Thu Jun 23 2011 - 05:43:49 CDT

• Next message: Hasan haska: "slow heating md"
• Previous message: divya nayar: "finding water around protein"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear all,

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
σ = -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
mica
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
is not
required by PME algorithm.

In addition, to eliminate the effect of mica images on protein, can PBC
be only
applied to two directions in NAMD?

Thanks in advance.

Best wishes,

yingzhe

-- 
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/

• Next message: Hasan haska: "slow heating md"
• Previous message: divya nayar: "finding water around protein"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:29 CST