[AMBER] Regarding to the parameters setup in SMD simulation

From: 辛志宏 <xzhfood.njau.edu.cn>
Date: Sat, 21 Nov 2020 16:35:00 +0800 (GMT+08:00)

Dear All,

I am going to simulated a SMD using LCOD by Amber as show in the Fig,

The distance between the water oxygen (1) and the carbonyl carbon (2) of the scissile bond was adopted as the reaction coordinate,

The main parameters is as follows:

type = LCOD ! Linear Combination of Distance

   i = (3,1,2,1)

   r = (1.0,-1.0)

   path = (distance(3,1), distance(2,1))

   harm = (1000.0)

   end variable

I wonder the i list and path is correct or not, any suggestion will be much appreciate.

Zhihong xin

College of Food Science and technology

Nanjing Agricultural University

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(image/png attachment: 11.png)

Received on Sat Nov 21 2020 - 01:00:02 PST
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