<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>The LJ-14 interaction is a two-body interaction,<br>one of which is apparently at a distance longer than the non-bonded cut-off.<br>mdrun determines the communication distances when starting<br>the simulation, see the md.log file for details.<br>Apparently all your bonded interactions are initially within<br>the non-bonded cut-off distance, but become longer<br>during the run.<br><br>You can set the bonded communication distance (as hinted<br>in the error message) with the mdrun option -rdd.<br>1 nm might already be enough, but the distance will no affect<br>the performance significantly (unless it prohibits certain<br>dd grid setups).<br><br>Berk<br><br><hr id="stopSpelling">Date: Wed, 19 Nov 2008 00:43:48 +0000<br>From: lastexile7gr@yahoo.de<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;" valign="top">Hello,<br><br>(I remind you that my initial system is a monoclinic crystal, which is a sub categorie to triclinic boxes)<br><br>compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in less steps than before, I face this:<br><br>Not all bonded interactions have been properly assigned to the domain decomposition cells<br><br>A list of missing interactions:<br> LJ-14 of 15408 missing 1<br><br>Molecule type 'molec'<br>the first 10 missing interactions, except for exclusions:<br> LJ-14 atoms 44 55 global 1881
1892<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.2<br>Source code file: domdec_top.c, line: 341<br><br>Fatal error:<br>1 of the 24208 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.74473 nm) or<br>the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br><br>I'm using the switch spline option and the second cut-off is the one I'm using. I do not know how the first cut-off is calculated. <br><br>Also I get messages about : correcting invalid box during the simulation.<br><br>Should I change anything to my files and/or to the options of grompp, and if the answer is affirmative which of them?<br><br>Thank you,<br>Nikos<br><br></td></tr></tbody></table><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>