<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>This was a new issue in 4.0, 3.3 was fine.<br><br>Berk<br><br>> Date: Wed, 18 Feb 2009 13:26:39 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff<br>> <br>> Thanks Berk, 4.0.4 does show the expected behaviour for me with the <br>> twin-range cutoff. Since I obtained 4.0.4 prior to mentioning this <br>> issue, I gather that you gave the free energy code a good looking-over <br>> recently. I really appreciate it.<br>> <br>> I have seen only one previous paper that utilized a twin-range cutoff <br>> for annihilation simulations, but that was done via gromos in 2003 <br>> (Lei and Smith, Biophys. J., 3513-3520, 2003) and since this part of <br>> the free-energy code in gromacs is done in C, not fortran, I expect <br>> that gromos annihilation simulations utilizing a twin-range cutoff are <br>> not necessarily subject to any of these issues.<br>> <br>> Thanks again,<br>> Chris.<br>> <br>> -- original message --<br>> <br>> Hi,<br>> <br>> I just fixed this in 4.0.4.<br>> The forces are always correct, dgdl in 4.0.3 was only correct at <br>> nstlist steps.<br>> <br>> Currently 4.0.4 is only available through ftp.<br>> We still need to add it (and the release notes) to the download page.<br>> <br>> Berk<br>> <br>> > Date: Tue, 17 Feb 2009 17:50:17 -0500<br>> > From: chris.neale at utoronto.ca<br>> > To: gmx-users at gromacs.org<br>> > Subject: [gmx-users] anomalous free energy dgdl.xvg values every <br>> > nstlist steps while using a twin-range cutoff Hello,<br>> ><br>> > I believe that the free-energy code dgdl contribution from the <br>> > twin-range cutoff is being calculated incorrectly in gromacs 4.0.3 <br>> > (and probably other versions as well).<br>> ><br>> > Specifically, I notice that the dgdl values spike at nstlist <br>> > intervals. This can be seen directly from my dgdl.xvg and also from <br>> > running g_analyze -ac.<br>> ><br>> > I suspect that while the forces from the LJ interactions that are in <br>> > the longer range of the twin-range are added every step while the <br>> > dgdl value is modified to have nstlist times these contributions <br>> > every nstlist step.<br>> ><br>> > My belief that the forces are truley added every step comes from <br>> > section 4.6.3 of the gromacs 4 manual:<br>> ><br>> > "In the neighbor list all interaction pairs that fall within rlist <br>> > are stored. Furthermore, the interactions between<br>> > pairs that do not fall within rlist but do fall within <br>> > max(rcoulomb,rvdw) are computed during NS, and the forces<br>> > and energy are stored separately, and added to short-range forces at <br>> > every time step between successive NS."<br>> ><br>> > Perhaps the long-range LJ component forces are actually applied to <br>> > the particles every nstlist steps as a force multipled by nstlist, <br>> > as is done in NAMD, but I am currently under the impression that <br>> > this is not the case.<br>> ><br>> > I am happy to provide more details and files if necessary, but <br>> > hopefully this information is sufficient for a skilled coder to take <br>> > a look and determine if this is indeed the case.<br>> ><br>> > Thank you,<br>> > Chris.<br>> -- snip --<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>