[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations

[xi zhao]

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?
thank you! 



--- 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>
> 
> --- *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: "Discussion list for GROMACS users" <gmx-users at 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>>
>      >
>      >
>      > 
>     -- ========================================
> 
>     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>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100324/d0346977/attachment.html>