Thanks for the reply.
With MD simulation, we hoping to fold the long chain of the protein before proceeding with screening the protein model with compounds.
Any input whether the high angstroms value is OK in this case?
Thank in advance.
Best regards,
Li Zhe
________________________________
From: Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
Sent: Thursday, 18 August, 2016 12:12:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSd
Hi.
We are just trying to fold the long chains of this protein.
Best regards,
Li Zhe
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, 18 August, 2016 12:11:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSd
hi
What do you want to learn from this type of simulation?
Hai
On Thu, Aug 18, 2016 at 12:08 AM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my
> wrote:
> Dear AMBER users,
>
>
> I am currently simulating a protein (1304 amino acids) in vacuo without
> restraints.
>
> >From the RMSd versus time plot, the RMSd is about 140 angstroms!
>
> I wonder is this observation still consider as normal?
>
> As from the tutorial, this is considered as 'blown up'.
>
> Any inputs will be much appreciated.
>
>
> Thank you.
>
>
> Best regards,
>
> Li Zhe
>
>
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>
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Received on Wed Aug 17 2016 - 23:00:02 PDT
