[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
> > 
> >     ========================================
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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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