<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>OK, so you have a stable simulation and the box corrections are caused by "diffusion"<br>of the box shape. This diffusion issue has been solved for Gromacs 4.0, where with<br>isotropic scaling the box shape is fixed.<br></div><br>But the actual problem causing the crashes has not been found yet.<br>I tried with a simple test system, but could not reproduce the error.<br>Could you provide me with a tpr file that crashes after a small amount of steps?<br>This should be possible by running a simulation that crashes with nstxout,nstvout<br>and nstenergy relatively high and then using tpbconv.<br><br>Berk.<br><br><hr id="stopSpelling">> Date: Thu, 27 Mar 2008 18:50:16 +0100<br>> From: reich@mpikg.mpg.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling<br>> <br>> Hi Berk,<br>> <br>> my volume fluctuations are relative small. For the largest and smallest<br>> system respectively that I have been simulating the statistics are:<br>> <br>> Average RMSD Fluct.<br>> 207.7 nm^3 0.699 nm^3 0.698 nm^3<br>> 75.1 nm^3 0.431 nm^3 0.432 nm^3<br>> <br>> My pressure coupling parameters are:<br>> <br>> ; Pressure coupling<br>> Pcoupl = Parrinello-Rahman<br>> pcoupltype = isotropic<br>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>> tau_p = 5.0<br>> compressibility = 5e-5<br>> ref_p = 1.0<br>> <br>> <br>> Best<br>> <br>> Luther<br>> <br>> > Hi,<br>> ><br>> > I am also starting to wonder now if you might have other problems.<br>> > Have you checked if there aren't very strong volume fluctuations?<br>> ><br>> > Could you mail your mdp pressure coupling parameters?<br>> ><br>> > Berk.<br>> ><br>> ><br>> >> Date: Thu, 27 Mar 2008 15:16:39 +0100<br>> >> From: reich@mpikg.mpg.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure<br>> >> coupling<br>> >><br>> >> Hi Berk,<br>> >><br>> >> I reran my simulations with the settings you suggested. Unfortunately<br>> >> most<br>> >> of them crashed. In some of them I received the original error message:<br>> >><br>> >> Source code file: ns.c, line: 313<br>> >><br>> >> Fatal error:<br>> >> Could not correct too skewed box<br>> >><br>> >> I did not, however, receive this message from all runs. In some cases<br>> >> conformations were written out for a few steps shortly before the run<br>> >> crashed, but the simulation process was killed before any error could be<br>> >> written out. The log-files no proper ending in these cases. Is there any<br>> >> way to get the error message before the simulation process is killed?<br>> >><br>> >> In one particular simulation the end of the log-file looked like this:<br>> >><br>> >> Correcting invalid box:<br>> >> old box (3x3):<br>> >> old box[ 0]={ 5.62033e+00, 0.00000e+00, 0.00000e+00}<br>> >> old box[ 1]={ 2.79637e+00, 5.26160e+00, 0.00000e+00}<br>> >> old box[ 2]={-2.81298e+00, -3.13776e-03, 4.54280e+00}<br>> >> new box (3x3):<br>> >> new box[ 0]={ 5.62033e+00, 0.00000e+00, 0.00000e+00}<br>> >> new box[ 1]={ 2.79637e+00, 5.26160e+00, 0.00000e+00}<br>> >> new box[ 2]={ 2.80735e+00, -3.13776e-03, 4.54280e+00}<br>> >><br>> >> t = 34154.008 ps: Water molecule starting at atom 1615 can not be<br>> >> settled.<br>> >> Check for bad cont<br>> >><br>> >><br>> >> I am not sure whether there is another problem with this simulation<br>> >> causing the crash. But since the crash occurred directly after the<br>> >> correction of the box I thought I should report this as well.<br>> >><br>> >><br>> >> Best<br>> >><br>> >> Luther<br>> <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>