Hi, Zhihong
What you are using is the old format before Amber16, I strongly recommend
you to
update to Amber18 or the latest Amber20 in which the new format should be
used to
apply the SMD module. It is more straightforward and easier to use.
Basically you need to define all the parameters of SMD inside &smd section
and store the info
of reaction coordinates in a separate file. You can check the usage in
AMBER20 manual section 23.4
and the following tutorial
http://ambermd.org/tutorials/advanced/tutorial31/index.php
Best
Feng
On Sat, Nov 21, 2020 at 3:35 AM 辛志宏 <xzhfood.njau.edu.cn> wrote:
> 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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 04 2020 - 18:00:02 PST
