Re: [AMBER] is it possible to run aMD in implicit water model?

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Tue, 22 Nov 2016 14:54:33 -0600

Hi Abhi,

It is possible to do that. Check $AMBERHOME/test/amd/rna_gb/ directory, there are examples there.

Kind regards,
Pengfei

> On Nov 22, 2016, at 2:51 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> Hi
>
> I am doing calculations in implicit water model, I want to know it is possible to run aMD with this implicit water model?
>
> If yes then how do I calculate the parameters for aMD? Will running simple production run explicitly and putting that value in it justify the calculations?
>
>
> Kindly suggest me how do I justify my calculation by this method.
>
>
>
> Thanking you,
>
> Abhishek
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