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 <jalem...@vt.edu> 写道： 发件人: Justin A. Lemkul <jalem...@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@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 /<jalem...@vt.edu>/* 写道： > > > 发件人: Justin A. Lemkul <jalem...@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@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@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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