<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>I just fixed this in 4.0.4.<br>The forces are always correct, dgdl in 4.0.3 was only correct at 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@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>> 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 (and <br>> probably other versions as well).<br>> <br>> Specifically, I notice that the dgdl values spike at nstlist intervals. <br>> This can be seen directly from my dgdl.xvg and also from running <br>> g_analyze -ac.<br>> <br>> I suspect that while the forces from the LJ interactions that are in the <br>> longer range of the twin-range are added every step while the dgdl value <br>> is modified to have nstlist times these contributions every nstlist step.<br>> <br>> My belief that the forces are truley added every step comes from section <br>> 4.6.3 of the gromacs 4 manual:<br>> <br>> "In the neighbor list all interaction pairs that fall within rlist are <br>> 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 the <br>> particles every nstlist steps as a force multipled by nstlist, as is <br>> done in NAMD, but I am currently under the impression that this is not <br>> the case.<br>> <br>> I am happy to provide more details and files if necessary, but hopefully <br>> this information is sufficient for a skilled coder to take a look and <br>> determine if this is indeed the case.<br>> <br>> Thank you,<br>> Chris.<br>> <br>> Relevant .mdp options:<br>> <br>> integrator = sd<br>> energygrps = SOL DPC DPN ; annihilated group must be <br>> separated<br>> gen_seed = -1<br>> comm_mode = linear<br>> nstcomm = 1<br>> comm_grps = System<br>> dt = 0.004<br>> nstlist = 5<br>> ns_type = grid<br>> pbc = xyz<br>> coulombtype = PME<br>> rcoulomb = 0.9<br>> fourierspacing = 0.12<br>> pme_order = 4<br>> vdwtype = cut-off<br>> rvdw_switch = 0<br>> rvdw = 1.4<br>> rlist = 0.9<br>> DispCorr = EnerPres <br>> Pcoupl = Berendsen ; REMOVE_FOR_EM<br>> pcoupltype = isotropic ; REMOVE_FOR_EM<br>> compressibility = 4.5e-5 ; REMOVE_FOR_EM<br>> ref_p = 1. ; REMOVE_FOR_EM<br>> tau_p = 4.0 ; REMOVE_FOR_EM<br>> tc_grps = System ; REMOVE_FOR_EM<br>> tau_t = 1.0 ; REMOVE_FOR_EM<br>> ld_seed = -1 ; REMOVE_FOR_EM<br>> ref_t = 300. ; REMOVE_FOR_EM<br>> gen_temp = 300. ; REMOVE_FOR_EM<br>> constraints = all-bonds ; REMOVE_FOR_EM<br>> constraint_algorithm= lincs ; REMOVE_FOR_EM<br>> lincs-iter = 1 ; REMOVE_FOR_EM<br>> lincs-order = 6 ; REMOVE_FOR_EM<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>