<HTML>
<HEAD>
<TITLE>Re: [gmx-users] Force constant for umbrella sampling potential</TITLE>
</HEAD>
<BODY>
<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Farzad,<BR>
The force constant is up to you to define in the .ppa file you create for umbrella sampling.<BR>
<BR>
I ask the question about the 0.5 term because I am using Grossfield’s WHAM algorithm and it assumes that the biasing potential used has a 0.5 in front, but I know for example CHARMM does not include the 0.5 and I just need to know if this is also the case with gromacs.<BR>
Thank you.<BR>
-Dina<BR>
<BR>
<BR>
On 12/17/07 12:34 AM, "Farzad Molani" <farzad_c81@yahoo.com> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Hi dear<BR>
I think it has got 0.5 in equation.<BR>
U=0.5*K(r-b)2<BR>
but I dont knoe how do I get K please help me<BR>
<BR>
<B><I>dtmirij <dtmirij@sandia.gov></I></B> wrote:<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'> 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>
Thank you in advance.<BR>
-Dina<BR>
<BR>
<BR>
_______________________________________________<BR>
gmx-users mailing list gmx-users@gromacs.org<BR>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><BR>
Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> 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 <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
<BR>
<BR>
<HR ALIGN=CENTER SIZE="1" WIDTH="100%">Never miss a thing. Make Yahoo your homepage. <a href="http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs"><http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs></a> <BR>
<HR ALIGN=CENTER SIZE="3" WIDTH="95%"></SPAN></FONT><FONT SIZE="2"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:10.0px'>_______________________________________________<BR>
gmx-users mailing list gmx-users@gromacs.org<BR>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><BR>
Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> 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 <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><BR>
</SPAN></FONT></FONT></BLOCKQUOTE><FONT SIZE="2"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:10.0px'><BR>
</SPAN></FONT></FONT>
</BODY>
</HTML>