<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Mr Justin A. Lemkul : </DIV>
<DIV> In fact, please read the document <A href="http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf">http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf</A>, the document shows the PMF can be reconstructed from the SMD, why?</DIV>
<DIV>thank you! <BR><BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank rel=nofollow><IMG class=pimg alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn" border=0></A><BR><BR>--- <B>10年3月24日，周三, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>发件人: Justin A. Lemkul <jalemkul@vt.edu><BR>主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations<BR>收件人: "Gromacs Users' List" <gmx-users@gromacs.org><BR>日期: 2010年3月24日,周三,下午10:10<BR><BR>
<DIV class=plainMail><BR><BR>xi zhao wrote:<BR>> dear Mr Justin A. Lemkul :<BR>> 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!_<BR>> _Thnak you!_<BR>> <BR><BR>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.<BR><BR>-Justin<BR><BR>> <BR>> 4 <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>><BR>> <BR>> --- *10年3月24日，周三, Justin A. Lemkul /<<A
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>/* 写道：<BR>> <BR>> <BR>> 发件人: Justin A. Lemkul <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>> 主题: Re: [gmx-users] how to reconstruct potentials of mean force<BR>> through time series analysis of SMD or pulling simulations<BR>> 收件人: "Discussion list for GROMACS users" <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> 日期: 2010年3月24日,周三,下午9:58<BR>> <BR>> <BR>> <BR>> xi zhao wrote:<BR>> > Dear gromacs
users:<BR>> ><BR>> > How to reconstruct potentials of mean force through time 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>> <A href="http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling" target=_blank>http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling</A><BR>> <BR>> -Justin<BR>> <BR>> ><BR>> > 4<BR>> <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844"
target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A><BR>> <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>>><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>> <A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR>> <BR>> ========================================<BR>> -- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>><BR>> <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before<BR>> posting!<BR>> Please don't post (un)subscribe requests to the list. Use the www<BR>> interface or send it to <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php"
target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><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><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search"
target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR></DIV></BLOCKQUOTE></td></tr></table><br>