<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">
<DIV class=plainMail>Hi</DIV>
<DIV class=plainMail> </DIV>
<DIV class=plainMail>Thank you Justin and Chris, for your comments and suggestions. </DIV>
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<DIV class=plainMail>All the restrained distances are less than half of the box length. The reason I want to use different box sizes is: g_wham gives zero value for the first bin, so I need extend my simulation for long restrant distances for the use of -zprof0 option to make the PMF zero. Unfortunately, after finished simulations for short restraints, I realized that the box size may not be long enough for the use of -zprof0. Therefore I think of using larger box sizes for the rest of the windows with longer restraints. As you suggested, I need to do a test of finite-size effect before switching to larger box sizes.</DIV>
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<DIV class=plainMail>Btw, for using g_wham, do I need to use the same parameters for different windows, e.g., the force constant, the simulation time and the width of the window?</DIV>
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<DIV>Cheers,</DIV>
<DIV>Li Jianguo</DIV>
<DIV>Research fellow</DIV>
<DIV>Singapore-MIT Alliance</DIV>
<DIV><SPAN class=yshortcuts id=lw_1259810471_0 style="BACKGROUND: none transparent scroll repeat 0% 0%; CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">National University of Singapore</SPAN></DIV>
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<DIV class=plainMail><BR>I have never heard of such a thing. Is the restraint distance always less than <BR>1/2 the box dimension in the pulling direction? If not, then this approach <BR>doesn't work.<BR><BR>I have always been under the impression that when running umbrella sampling, you <BR>have to actually be doing sampling in different regions of configurational space <BR>in the same system, in order to get a continuous energy function and appropriate <BR>sampling.<BR><BR>-Justin<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><BR><BR><BR><BR>Message: 4<BR>Date: Wed, 02 Dec 2009 08:42:36 -0500<BR>From: <A href="http://us.mc1114.mail.yahoo.com/mc/compose?to=chris.neale@utoronto.ca" ymailto="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</A><BR>Subject: [gmx-users] PMF calculation using g_wham using different<BR> simulation boxes<BR>To: <A href="http://us.mc1114.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID: <<A href="http://us.mc1114.mail.yahoo.com/mc/compose?to=20091202084236.bk7yqoke0w0wcwcs@webmail.utoronto.ca" ymailto="mailto:20091202084236.bk7yqoke0w0wcwcs@webmail.utoronto.ca">20091202084236.bk7yqoke0w0wcwcs@webmail.utoronto.ca</A>><BR>Content-Type: text/plain;
charset=ISO-8859-1; DelSp="Yes";<BR> format="flowed"<BR><BR>Hi Li,<BR><BR>In my opiniun, what you propose is acceptable, but not rigorous, and <BR>you will need to prove that there are no unexpected artifacts of <BR>changing box size. For example, you should definitely run a couple of <BR>your small box systems as larger boxes as well and show that you get <BR>the same histograms for the distances between your polyatomic particles.<BR><BR>Justin is correct about the need for a box that is 2x larger than your <BR>displacement, and pull_pbcatom is an important option to set as well.<BR><BR>Chris.<BR></DIV></BLOCKQUOTE></td></tr></table><br>