Can you tell us more about what you mean by "the potential energy surface
of the protein"? Are you trying to reproduce something that you have seen
in a publication? You can obtain free energy surfaces, but you would need
to decide what coordinates to use for mapping the potential of mean force,
and that depends a lot on what you did in these remd simulations, how well
converged they are, and especially what you are trying to learn. Without
knowing that it isn't possible to help other than to tell you to use a
program like cpptraj to extract data from each snapshot, and if you want
free energies, convert the histograms fractions to relative free energies.
If you really want potential energies, they are in the output file already,
but I suspect that that is not really what you want.
Hope that helps.
On Dec 21, 2014 7:13 PM, "Wang Moye" <wangmoye13.mails.ucas.ac.cn> wrote:
>
>
>
> -----原始邮件-----
> 发件人: "Wang Moye" <wangmoye13.mails.ucas.ac.cn>
> 发送时间: 2014年12月16日 星期二
> 收件人: amber <amber.ambermd.org>
> 抄送:
> 主题: How to analyze REMD results
>
>
>
>
> Hello everyone,
> I am a new Amber user.I have finished the REMD simulaitons using Amber12
> version. The jobs was frequently restarted for long simulations. Now I
> want to obtain the potential energy surface of the protein. How can I deal
> with the several stages of data? Which tool should I use?
> By the way, I have read the Amber tutorials and I could extract
> temperature trajectories .But I didn't know how to analyze them for
> obtaining the whole potential energy surface. Thank you!
>
> Wang moye
> University of Chinese Academy of Sciences
>
>
>
>
>
>
>
>
>
> --
> 王漠野
>
>
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Received on Sun Dec 21 2014 - 19:30:02 PST
