[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 15:44:39 CET 2010
xi zhao wrote:
> Dear Mr Justin A. Lemkul :
> Thank you for your advice, can you give more suggetions?
> Thank you very much!
Not really. If you search "Jarzynski" in the mailing list archives, you get 8
results, indicating to me that this is not a particularly popular way to
calculate free energy changes with Gromacs.
There are inherent limitations to the technique, in that you are trying to
derive equilibrium data from non-equilibrium trajectories (hence why umbrella
sampling is preferred). Jarzynski's method is sensitive to the pull rate and
number of pulls conducted. To be very accurate, you have to pull infinitely
slowly an infinite number of times (not possible, clearly), but you may be able
to converge the results within a reasonable error estimate if you repeat the
pulling many, many times (this could mean 10, 50, or 1000 times, depending on
what it is that you're doing). There are several papers out there that have
analyzed this phenomenon in the context of both of these variables.
-Justin
>
> 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
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> >
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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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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