<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>I don't know why I did not add checks for ld-seed before.<br>Now grompp gives a note when continutation=yes and ld-seed!=-1.<br><br>tpbconv will now generate a new ld-seed when reading a trajectory<br>(but you should not use tpbconv, use a checkpoint file instead).<br><br>But yesterday I forgot to tell that there is a bug in the checkpointing<br>of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box<br>size would always be stored in the checkpoint file, which causes problems<br>with NPT simulations. NPT simulations with domain decomposition and<br>all NVT simulations were fine.<br><br>Gromacs 4.0.4 will all bugs fixed and extra checks should be released today.<br><br>Berk<br><br>> Date: Wed, 4 Feb 2009 19:30:47 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator<br>> <br>> It appears as if you were correct Berk. I will report on the results of my 24h test tomorrow, but I also set up another system <br>> that used ld_seed=1993 and ran in 20 ps segments instead of the 200 ps segments that I was previously using. This system shows <br>> signs of disaggregation on the 200 ps time-scale as opposed to the 2 ns time-scale that I observed for 200 ps segments.<br>> <br>> I don't know how you figured that one out, but I am very grateful.<br>> <br>> Now that I see the trajectories, it does make sense that any net movement applied to an individual molecule by the noise will <br>> lead to directed movement over many separate segments.<br>> <br>> I think this is probably worth a note in the grompp output for sd runs when a user sets ld_seed to something other than -1 and <br>> utilizes the -t option (or some other indication that this is intended as a continuation).<br>> <br>> Chris.<br>> <br>> -- original message --<br>> <br>> Thank you Berk,<br>> <br>> I will repeat my runs using the checkpoint file and report my findings back to this list. Thank you for this advice.<br>> <br>> Chris.<br>> <br>> -- original message --<br>> <br>> Hi,<br>> <br>> In this manner you use the same random seed and thus noise for all parts.<br>> In most cases this will not lead to serious artifacts with SD,<br>> but you can never be sure.<br>> When checkpoints are used, you do not repeat random numbers.<br>> This also gives a difference between serial and parallel in 4.0.<br>> With serial you get exactly the same noise per atom, in parallel not,<br>> since atoms migrate from one node to another (with domain decompostion).<br>> <br>> If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.<br>> <br>> Berk<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>