[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Berk Hess
gmx3 at hotmail.com
Wed Mar 24 16:55:02 CET 2010
Ah, I can make some advertisement for my own work again.
If you can do equilibrium simulations these will always be more efficient
than non-equilibrium, as Justin also pointed out below.
I have published a case where you can not (or not efficiently) do equilibrium
simulations, because you don't know the end state, then non-equilibrium
simulations are really useful, otherwise not:
http://pubs.acs.org/doi/abs/10.1021/ma702070n
Berk
> Date: Wed, 24 Mar 2010 10:48:18 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
>
>
>
> 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
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org
> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
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> > Please search the archive at http://www.gromacs.org/search before
> > posting!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
>
> --
> ========================================
>
> 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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