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Ah, I can make some advertisement for my own work again.<br>If you can do equilibrium simulations these will always be more efficient<br>than non-equilibrium, as Justin also pointed out below.<br>I have published a case where you can not (or not efficiently) do equilibrium<br>simulations, because you don't know the end state, then non-equilibrium<br>simulations are really useful, otherwise not:<br>http://pubs.acs.org/doi/abs/10.1021/ma702070n<br><br>Berk<br><br>> Date: Wed, 24 Mar 2010 10:48:18 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations<br>> <br>> <br>> <br>> xi zhao wrote:<br>> > <br>> > Dear Mr Justin A. Lemkul :<br>> > In fact, please read the document <br>> > http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf, <br>> > the document sho
ws the PMF can be reconstructed from the SMD, why?<br>> <br>> I never disputed that fact. Please the post I just sent you. The conclusions <br>> of the paper indicate that umbrella sampling is more robust and costs less time, <br>> although, if conducted properly, SMD can yield similar results.<br>> <br>> -Justin<br>> <br>> > thank you!<br>> > <br>> > 4 <br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844><br>> > <br>> > --- *10Äê3ÔÂ24ÈÕ£¬ÖÜÈý, Justin A. Lemkul /<jalemkul@vt.edu>/* дµÀ£º<br>> > <br>> > <br>> > ·¢¼þÈË: Justin A. Lemkul <jalemkul@vt.edu><br>> > Ö÷Ìâ: Re: [gmx-users] how to reconstruct potentials of mean force<br>> > through time series analysis of SMD or pulling simulations<br>> > ÊÕ¼þÈË: "Gromacs Users' List" <gmx-users@gromacs.org><br>> &g
t; ÈÕÆÚ: 2010Äê3ÔÂ24ÈÕ,ÖÜÈý,ÏÂÎç10:10<br>> > <br>> > <br>> > <br>> > xi zhao wrote:<br>> > > dear Mr Justin A. Lemkul :<br>> > > I have read your _tutorial ,it is suitable for umbrella sampling<br>> > method, it is not for SMD, wham or g_wham can not be used!_<br>> > > _Thnak you!_<br>> > ><br>> > <br>> > If you want to use SMD trajectories to calculate free energy<br>> > changes, you will need Jarzynski's inequality and a large amount of<br>> > sampling. I do not think such a method is implemented in Gromacs;<br>> > you may have to write your own scripts to do this.<br>> > <br>> > -Justin<br>> > <br>> > ><br>> > > 4<br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844<br>> > <
;http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>><br>> > ><br>> > > --- *10Äê3ÔÂ24ÈÕ£¬ÖÜÈý, Justin A. Lemkul /<jalemkul@vt.edu<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* дµÀ£º<br>> > ><br>> > ><br>> > > ·¢¼þÈË: Justin A. Lemkul <jalemkul@vt.edu<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>><br>> > > Ö÷Ìâ: Re: [gmx-users] how to reconstruct potentials of mean force<br>> > > through time series analysis of SMD or pulling simulations<br>> > > ÊÕ¼þÈË: "Discussion list for GROMACS users"<br>> > <gmx-users@gromacs.org<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>><br>> > > ÈÕÆÚ: 2010Äê3ÔÂ24ÈÕ,Ö
ÜÈý,ÏÂÎç9:58<br>> > ><br>> > ><br>> > ><br>> > > xi zhao wrote:<br>> >
> > Dear gromacs users:<br>> > > ><br>> > > > How to reconstruct potentials of mean force through time<br>> > series<br>> > > analysis of SMD or pulling simulations; for example, software or<br>> > > script using, how to reconstruct PMF in detail?<br>> > > > thank you very much!<br>> > > ><br>> > ><br>> > > http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling<br>> > ><br>> > > -Justin<br>> > ><br>> > > ><br>> > > > 4<br>> > > <br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844<br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=70
3fa929658518b2720b087c59cd85f2dabf8844><br>> > > <br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844<br>> > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>><br>> > > ><br>> > > ><br>> > > ><br>> > > -- ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > MILES-IGERT Trainee<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http:
//www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > -- gmx-users mailing list gmx-users@gromacs.org<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org><br>> > > <br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org><br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before<br>> > > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the www<br>> > > interface or send it to gmx-users-request@gromacs.org<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org><br>> > > <br>> > <http://cn.mc151.mail.yahoo.
com/mc/compose?to=gmx-users-request@gromacs.org>.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > ><br>> > ><br>> > > <br>> > <br>> > -- ========================================<br>> > <br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > <br>> > ========================================<br>> > -- gmx-users mailing list gmx-users@gromacs.org<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org><br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>>
> Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > Please don't post (
un)subscribe requests to the list. Use the www<br>> > interface or send it to gmx-users-request@gromacs.org<br>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br
>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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