Thank you so much,
but I have a small doubt that how does it calculate ethreshp, alphap, ethreshd,alphad values for this calculation.
Do we need to run MD in exlicit water model and then calculate ethreshp, alphap, ethreshd,alphad values for implicit aMD?
________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: Tuesday, November 22, 2016 9:54:33 AM
To: AMBER Mailing List
Subject: Re: [AMBER] is it possible to run aMD in implicit water model?
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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Received on Tue Nov 22 2016 - 15:00:02 PST
