[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 24 15:48:18 CET 2010
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
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *10年3月24日，周三, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道：
>
>
> 发件人: Justin A. Lemkul <jalemkul at 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 at 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
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> >
> > --- *10年3月24日，周三, Justin A. Lemkul /<jalemkul at vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* 写道：
> >
> >
> > 发件人: Justin A. Lemkul <jalemkul at vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@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 at gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@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
> >
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> >
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
> > >
> > >
> > >
> > -- ========================================
> >
> > 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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