<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: bjorn.sathre@student.uib.no<br>Subject: RE: [gmx-users] Possible issues with CVS pull code 200800508<br>Date: Fri, 6 Jun 2008 09:41:36 +0200<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 body.EC_hmmessage
{font-size:10pt;font-family:Tahoma;}
</style>
<div style="text-align: left;">Hi,<br><br>Larger time step or higher constraint will not help.<br></div><br>I assume you do not need the walls for interactions,<br>you only use them for efficient neighbor search, right?<br><br>The distance should not fluctuate at all, so there is something very wrong.<br><br>One problem is that you pressure couple in z.<br>This might be the cause of all your problems.<br>Try setting the compressibility in z to zero.<br><br>Berk.<br><br><br><hr id="EC_stopSpelling">> Date: Thu, 5 Jun 2008 13:42:39 +0200<br>> From: st01397@student.uib.no<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Possible issues with CVS pull code 200800508<br>> <br>> I am doing Constraint force pulling to measure the cohesive force<br>> between two rectangular slabs of a certain material. The slabs are<br>> made effectively infinite in the directions normal to z, using pbc=3Dxy,<br>> I have to use walls to be able to exploit PME eletrostatics. To<br>> accomplish this I have to use walls in the z-direction<br>> My box size is 3.4x3.4x15 nm, the two slabs are each slightly<br>> elongated rectangular "prisms" 3.4x3.4x5.1 nm, comprising about 7500 =20<br>> atoms each separated by say, 1 nm initially. Thus about 1/3 of the =20<br>> box was vacuum outside the "external" faces of the slabs.<br>> <br>> My auxiliary files are stored at http:/drop.io/gmxpull<br>> <br>> My paramater-file is eq_pull.mdp<br>> <br>> During the course of the simulation, the slabs stay separated at all<br>> times, but show appreciable oscillation in distance the constraint<br>> forces between the COM's of the two slabs show the peculiar behaviour<br>> shown in the file:<br>> <br>> pullforces.xvg<br>> <br>> It seems as if the constraint forces simply becomes to great, <br>> especially at short separations, and<br>> makes the system unstable. Should I increase or decrease the pull_constr_tol<br>> to improve the stability of force readouts in my large system? I would <br>> presume increasing the tolerance would promote less fluctuations in <br>> forces, and larger distance fluctuations?<br>> I know that the constraint Force is calculated as F = M (dr)/(dt)^2, <br>> where dr is the adjustment made by the constraint algorithm(SHAKE) and <br>> dt is the time-step during which the constraining takes place. This <br>> leads me to anticipate that maybe a larger time-step would promote <br>> stability?<br>> <br>> Determinig the COM forces along z with g_traj I get the output of:<br>> <br>> forces.xvg<br>> <br>> Why the strange behaviour of the constraint forces?<br>> Why the extreme peaks in forces? Why does the constraint force output<br>> and the output of force z-coordinate in "g_traj -com -nox -noy", differ so<br>> appreciably?<br>> <br>> <br>> Regards<br>> <br>> -- <br>> Bjørn Steen Sæthre<br>> PhD-student<br>> Insitute of Physics & Tech.- University of Bergen<br>> Allegt. 55,<br>> 5007 Bergen<br>> Norway<br>> <br>> Tel(office): +47 55582869<br>> Cell: +47 99253386<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="_blank">MSN Messenger</a>
</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>