<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><blockquote><hr id="EC_stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling<br>Date: Fri, 7 Mar 2008 10:14:00 +0100<br><br>
<meta http-equiv="Content-Type" content="text/html; charset=unicode">
<meta name="Generator" content="Microsoft SafeHTML">
<style>
.ExternalClass .EC_hmmessage P
{padding:0px;}
.ExternalClass EC_body.hmmessage
{font-size:10pt;font-family:Tahoma;}
</style>
<div style="text-align: left;"><br></div><br><br><br><hr id="EC_stopSpelling">> Date: Thu, 6 Mar 2008 13:57:31 +0100<br>> From: stephane.teletchea@jouy.inra.fr<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling<br>> <br>> Berk Hess a écrit :<br>> > Hi,<br>> > <br>> > I now realized that my fix what completely incorrect.<br>> > I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.<br>> > But my mistake means that is now given an error when the off diagonal<br>> > element is relatively more than 1 instead of more than 0.5.<br>> > This is a far too weak check.<br>> > So I would not expect any fatal errors any more with this incorrect check.<br>> > Therefore I don't understand why you still get errors.<br>> > <br>> > Could you try changing BOX_MARGIN to 0.5005, as it currently is in <br>> > version 4.0?<br>> > <br>> > Berk. <br>> <br>> We thus need a hot fix for 3.3.3?<br><br>A too weak check does, by itself, not cause problems.<br>It does mean that the check is useless, but Gromacs<br>by itself never generates incorrect boxes.<br><br>The problem with the check is still there, but it only<br>seem to occur very rarely.<br>I'll fix it properly in the CVS 3.3 patches branch.<br><br>Hi Luther,<br><br>To be sure that this time I really fix the problem,<br>could you apply the following changes and check if the problem is gone?<br><br>Thanks,<br><br>Berk.<br><br>diff -r1.34.2.3 pbc.h<br>51,52c51,53<br>< #define BOX_MARGIN 0.5001<br>< /* margin factor for checking if the box is too skewed */<br>---<br>> /* Margin factor for error message and correction if the box is too skewed */<br>> #define BOX_MARGIN 0.5010<br>> #define BOX_MARGIN_CORRECT 0.5005<br><br>diff -r1.57.2.9 pbc.c<br>100,102c100,102<br>< else if ((fabs(box[YY][XX]) > 2*BOX_MARGIN*box[XX][XX]) ||<br>< (fabs(box[ZZ][XX]) > 2*BOX_MARGIN*box[XX][XX]) ||<br>< (fabs(box[ZZ][YY]) > 2*BOX_MARGIN*box[YY][YY]))<br>---<br>> else if ((fabs(box[YY][XX]) > BOX_MARGIN*box[XX][XX]) ||<br>> (fabs(box[ZZ][XX]) > BOX_MARGIN*box[XX][XX]) ||<br>> (fabs(box[ZZ][YY]) > BOX_MARGIN*box[YY][YY]))<br><br>
retrieving revision 1.84.2.8<br>diff -r1.84.2.8 ns.c<br>251c251<br>< while (box[v][d] > BOX_MARGIN*box[d][d]) {<br>---<br>> while (box[v][d] > BOX_MARGIN_CORRECT*box[d][d]) {<br>261c261<br>< while (-box[v][d] > BOX_MARGIN*box[d][d]) {<br>---<br>> while (-box[v][d] > BOX_MARGIN_CORRECT*box[d][d]) {<br><br></blockquote><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>