<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;">Hi,<br><br>Did you check how your box dimensions evolve?<br><br>For a homogeneous system (as your small test system)<br>one should not use semi or anisotropic pressure coupling,<br>since the box shape can distort unlimitedly causing<br>the system to crash.<br><br>Berk.<br><br></div><br><hr id="stopSpelling">> Date: Tue, 3 Jun 2008 17:00:14 +0200<br>> From: till@bph.rub.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] neighborsearching in semiisotropic systems<br>> <br>> Dear users,<br>> <br>> During protein simulations occurred the range checking error of the <br>> neighborsearching. I checked the comments on this mistake in the user <br>> list and then checked my system on any hints of an exploding system but <br>> it seems to be stable. In order to be sure I cut down the system to a <br>> small peptide consisting of only ten aminoacids and used the ffG43a1 <br>> forcefield.<br>> <br>> <br>> I performed 10ns simulations of this small system in a cubic <br>> spc-waterbox with different pressure parameters and tried single and <br>> double precision. I got the following results:<br>> <br>> <br>> For<br>> <br>> pcoupltype = semiisotropic<br>> <br>> tau_p = 0.5 0.5<br>> <br>> compressibility = 4.5E-5 4.5E-5<br>> <br>> ref_p = 1 1<br>> <br>> <br>> with double precision occurred the mistake:<br>> <br>> <br>> -------------------------------------------------------<br>> <br>> Program mdrun_d.mpi, VERSION 3.3.1<br>> <br>> Source code file: nsgrid.c, line: 226<br>> <br>> <br>> Range checking error:<br>> <br>> Explanation: During neighborsearching, we assign each particle to a grid<br>> <br>> based on its coordinates. If your system contains collisions or parameter<br>> <br>> errors that give particles very high velocities you might end up with some<br>> <br>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>> <br>> put these on a grid, so this is usually where we detect those errors.<br>> <br>> Make sure your system is properly energy-minimized and that the potential<br>> <br>> energy seems reasonable before trying again.<br>> <br>> <br>> Variable ci has value 284. It should have been within [ 0 .. 200 ]<br>> <br>> Please report this to the mailing list (gmx-users@gromacs.org <br>> <mailto:gmx-users@gromacs.org>)<br>> <br>> <br>> Then, I changed tau_p to 5.0 and the mistake did not occurce anymore <br>> during the 10 ns. With single precision the mistake never occurres. I <br>> also tested double precision with pcoupltype = isotropic and this also <br>> works.<br>> <br>> Next, I wanted to reproduce the mistake so I took the same tpr file of <br>> the crashed simulation with tau_p = 0.5 and started the simulation <br>> again. The mistake occurred again but not at the same timestep. The <br>> first run crashed after step 1558630 and the second run after step <br>> 2597500 and also the ci variable is not exactly the same (Variable ci <br>> has value 283. It should have been within [ 0 .. 200 ]).<br>> <br>> <br>> I think there might be a problem between the neighborsearching and the <br>> semiisotropic pressurcoupling together with double precision. I am quite <br>> sure that the peptide is not the problem. Maybe there is a problem with <br>> a water molecule. I would be glad if someone can give me an explanation <br>> why this mistake is not reproducable at the same timestep and why it <br>> occures with tau_p=0.5 and not with tau_p=5.0.<br>> <br>> <br>> Thanks<br>> <br>> <br>> Till<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>