<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>If you are talking about equilibrium methods, for instance free energy intergration<br>or Bennett's acceptance ratio, there is no directionality.<br>You might start a simulations at a lamba point with the end configuration of the previous lambda,<br>which could introduce some directionality, but then you should equilibrate long enough<br>to see no effect of this.<br><br>If you are doing non-equilibrium methods, than I would say that it is common sense<br>that you should start from the higher entropy state, since starting from the lower<br>entropy state increase the probability that you miss a significant part of the phase<br>space of the other state.<br><br>Berk<br><br>> Date: Thu, 12 Mar 2009 22:18:25 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] free energy coupling/decoupling equivalence<br>> <br>> Hello,<br>> <br>> I have just read an interesting paper suggesting that the reference state in<br>> free energy decoupling/coupling simulations should be the one with larger<br>> entropy. Lu and Kofke "Accuracy of free-energy perturbation calculations in<br>> molecular simulation. I. Modeling" JCP V. 114, N. 17 pp. 7303-7311 (2001).<br>> <br>> I have seen some mention that:<br>> <begin quote><br>> Ordinarily, one would expect that "forward" and "reverse" only are<br>> meaningful when you're (a) doing nonequilibrium simulations, or (b)<br>> beginning simulations at lambda values from the ending configurations<br>> at preceding lambda values.<br>> <end quote><br>> http://www.gromacs.org/pipermail/gmx-users/2008-February/032430.html<br>> <br>> And now I am confused, since I would have thought that this was an important<br>> "forward" vs. "reverse" difference, although I may have my terminology <br>> wrong here.<br>> <br>> To put my questions succinctly:<br>> <br>> 1. In the gromacs implementation, is there any important difference<br>> between coupling and decoupling? I avoid the terms "forwrad" and<br>> "reverse" in order to avoid non-equilibrium or slow-growth connotations.<br>> <br>> 2. Does soft-core work properly for both LJ coupling and LJ decoupling?<br>> I am not clear how mdrun knows whether to soft-core lambda or 1-lambda<br>> since it is near the decoupled state that really needs the soft-core,<br>> and this could be at lambda or 1-lambda.<br>> <br>> Background information:<br>> I am doing coulomb and LJ separately; LJ only with soft-core; coulomb <br>> first in the decoupling. Everything is working fine for me in the <br>> decoupling department, but I am now considering switching to coupling <br>> as opposed to decoupling based on this Lu 2001 paper and am interested <br>> if anybody has some comments.<br>> <br>> Thank you,<br>> Chris.<br>> <br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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>
</html>