Re: Unfolding protocol..

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Fri Aug 03 2007 - 01:35:01 CDT

oops typos on the timesteps:

On 8/3/07, Arun Krishnan <krishnan_at_ttck.keio.ac.jp> wrote:
>
> Dear All,
>
> I am trying to unfold a small protein and here is what I think the
> protocol is. I would appreciate it if someone knowledgeable about unfolding
> simulations could let me know if this is ok or not:
>
> Steps:
>
> NPT
> ====
> Input: Protein in water box (periodic boundary conditions)
> (a) Energy minimization of protein + water box - 3 ps - 1fs timestep
> (b) heat to 300K - 7ps - 1fs timestep
> (c) equilibrate @ 300K - 1ns - 2fs timestep
> (d) Heat to 500K - 7ps - 1fs timestep
> (e) equilibrate @ 500K - 1ns - 2fs timestep
>
> NVT
> ===
>
> production run for 8ns - 2fs time step
>
>
> Questions:
>
> (1) Should I do an energy minimization before the production run in NVT?
> (2) Should the equilibration at 500K be done under NVT conditions?

    (3) Should the times to heat to 300K and 500K be > 7ps? If so how much?

Any help will be much appreciated.
>
> Regards,
>
> Arun
>
> --
> ***********************************************
> Arun Krishnan, Ph.D,
> Assistant Professor,
> Institute for Advanced Biosciences,
> Keio University,
> Center Building,
> Tsuruoka, Yamagata 997-0035
> Japan
> Phone: +81 (0)235-29-0824
> Email: krishnan_at_ttck.keio.ac.jp<https://mail.google.com/mail?view=cm&tf=0&to=krishnan@ttck.keio.ac.jp>
> URL: http://www.iab.keio.ac.jp/~krishnan>
> **********************************************

-- 
***********************************************
Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Japan
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
URL: http://www.iab.keio.ac.jp/~krishnan
**********************************************

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