Hi Pengfei
Thank you so much.
I really appreciate your help
Thanking you,
Abhishek
Sent using OWA for iPhone
________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: Tuesday, November 22, 2016 1:58:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] is it possible to run aMD in implicit water model?
Hi Abhi,
I think so. I checked the Run.gb.amd1 script and mdout.gb.amd1.save output file and found similar rules applied (as shown in page 383 of Amber16 manual: https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_doc12_Amber16.pdf&d=DgICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=J1BJ6ceZidrkJsOqZEWQ1YbJHwu6_-lb3yz2w4ExKrQ&s=_iI_-75Rztg8S2zdhNC9ct1P94P4lArsfa_YU3ryUuM&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_doc12_Amber16.pdf&d=DgICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=J1BJ6ceZidrkJsOqZEWQ1YbJHwu6_-lb3yz2w4ExKrQ&s=_iI_-75Rztg8S2zdhNC9ct1P94P4lArsfa_YU3ryUuM&e= >).
Kind regards,
Pengfei
> On Nov 22, 2016, at 4:36 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> 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 - 18:00:03 PST
