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Hi,<br><br>Gromacs has the half as a pre-factor in the potential.<br><br>Note that in 4.0.5 there is a g_wham program which can automatically<br>do the WHAM analysis on the mdrun output.<br><br>Berk<br><br>> Date: Tue, 1 Sep 2009 13:19:32 +0800<br>> From: mircial@sjtu.edu.cn<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Force constant for umbrella sampling potential<br>> <br>> Hello everyone,<br>> <br>> I would like to know does the harmonic biasing potential for running<br>> umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term<br>> incorporated into the force constant value that we specify?<br>> On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2.<br>> <br>> I am using Grossfieldã] WHAM<br>> algorithm and it assumes that the biasing potential used has a 0.5 in front,<br>> but I know for example CHARMM does not include the 0.5 and I just need to<br>> know if this is also the case with gromacs
<br>> <br>> Thank you in advance.<br>> <br>> R-X Gu<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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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