xi zhao wrote:
Dear Mr Justin A. Lemkul :
In fact, please read the document
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf,
the document shows the PMF can be reconstructed from the SMD, why?
I never disputed that fact. Please the post I just sent you. The conclusions
of the paper indicate that umbrella sampling is more robust and costs less time,
although, if conducted properly, SMD can yield similar results.
-Justin
thank you!
4
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--- *10年3月24日，周三, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
发件人: Justin A. Lemkul <jalem...@vt.edu>
主题: Re: [gmx-users] how to reconstruct potentials of mean force
through time series analysis of SMD or pulling simulations
收件人: "Gromacs Users' List" <gmx-users@gromacs.org>
日期: 2010年3月24日,周三,下午10:10
xi zhao wrote:
> dear Mr Justin A. Lemkul :
> I have read your _tutorial ,it is suitable for umbrella sampling
method, it is not for SMD, wham or g_wham can not be used!_
> _Thnak you!_
>
If you want to use SMD trajectories to calculate free energy
changes, you will need Jarzynski's inequality and a large amount of
sampling. I do not think such a method is implemented in Gromacs;
you may have to write your own scripts to do this.
-Justin
>
> 4
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>
> --- *10年3月24日，周三, Justin A. Lemkul /<jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
>
>
> 发件人: Justin A. Lemkul <jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
> 主题: Re: [gmx-users] how to reconstruct potentials of mean force
> through time series analysis of SMD or pulling simulations
> 收件人: "Discussion list for GROMACS users"
<gmx-users@gromacs.org
<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
> 日期: 2010年3月24日,周三,下午9:58
>
>
>
> xi zhao wrote:
> > Dear gromacs users:
> >
> > How to reconstruct potentials of mean force through time
series
> analysis of SMD or pulling simulations; for example, software or
> script using, how to reconstruct PMF in detail?
> > thank you very much!
> >
>
> http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling
>
> -Justin
>
> >
> > 4
>
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>
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> >
> >
> >
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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