<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>Are you running NPT, single processor with 4.0.3?<br>Then you are experiencing the bug that the box is not updated in the checkpoint file.<br>Please change to 4.0.4.<br><br>Berk<br><br><hr id="stopSpelling">From: guogj@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] About the binary identical continuation by        restarting        from the checkpoint file<br>Date: Tue, 24 Feb 2009 08:37:38 +0000<br><br>
<style>
.ExternalClass .EC_hmmessage P
{padding:0px;}
.ExternalClass body.EC_hmmessage
{font-size:10pt;font-family:Verdana;}
</style>
Hi, Mark,<br>
<br>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">I reduce the length of test runs to only 6 steps now. The binary identical continuation still cannot be obtained. I use gmxcheck to compare the results according to your suggestions and I find two reasons to cause different trajectories. </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">One is a water molecule happening to span the Y-boundary of the simulation box. In the undivided run, the molecule locates at the +Y direction while it occurs at the –Y direction in the continuous run. The differences of Y-coordinates are exactly the box length. Certainly, X and Z coordinates in the two runs are indeed identical. </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">The other one is the velocities of many atoms being different in the fifth or sixth digits. The case becomes more and more serious with time. </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">After I change the different initial gro files, the first phenomenon disappears because no spanning-boundary water occurs. However, the second one is always there no matter which Gromacs is used, the single-precision or the double-precision. So, my question is how to obtain the binary identical continuation. </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US"> </span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">regards,</span></p>
<p class="EC_MsoNormal" style=""><span style="font-size: 10pt; color: rgb(68, 68, 68); font-family: Verdana;" lang="EN-US">Guang-Jun</span></p>
<br>
<br><BR>> Date: Mon, 23 Feb 2009 14:37:06 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] About the binary identical continuation by restarting from the checkpoint file<br>> <br>> GuoGuangjun wrote:<br>> > Hi, All<br>> > <br>> > <br>> > <br>> > Before to perform long simulations, I think it is necessary to do <br>> > continuous runs. I make several tests<br>> > <br>> > to check the reliability of restart by using the checkpoint file. First, <br>> > I do a 6ps-long run, and then do it<br>> > <br>> > again by two parts, that is, the first half (3 ps) starts from the same <br>> > initial gro file, followed by its<br>> > <br>> > second half. Here are my operations:<br>> > <br>> > <br>> > <br>> > grompp -f 6ps1.mdp -c water.gro -p water.top -o 6ps1.tpr<br>> > <br>> > mpirun -np 4 mdrun -s 6ps1.tpr -o 6ps1.trr -x 6ps1.xtc -e 6ps1.edr -dlb no<br>> > <br>> > <br>> > <br>> > grompp -f 3ps.mdp -c water.gro -p water.top -o 3ps.tpr<br>> > <br>> > mpirun -np 4 mdrun -s 3ps.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb <br>> > no -cpo 3ps.cpt<br>> > <br>> > <br>> > <br>> > tpbconv -s 3ps.tpr -extend 3.0 -o 6ps2.tpr -cont<br>> > <br>> > mpirun -np 4 mdrun -s 6ps2.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb <br>> > no -cpi 3ps.cpt -append<br>> > <br>> > <br>> > <br>> > The log file tells me----“Restarting from checkpoint, appending to <br>> > previous log file.” However, when I<br>> > <br>> > check the binary files, such as 6ps1.trr and 6ps2.trr, the cmp command <br>> > tells me they are not identical.<br>> <br>> Use gmxcheck for this test. This will give you either confirmation that<br>> you're achieving your objective, or enough information to find out why not.<br>> <br>> > During these tests, I have turned off the gen_vel, optimize_fft, and <br>> > dynamic load balancing (dlb) according<br>> > <br>> > to Gromacs manual and previous posters. How to obtain the binary <br>> > identical continuation? My computational<br>> > <br>> > environments are Gromacs 4.0.3, lammpi 7.1.4, Redhat Linux, two AMD <br>> > Opteron CPUs with dual cores<br>> > <br>> > in each, 500 SPC water molecules, and the NPT ensemble.<br>> <br>> Your approach looks right to me.<br>> <br>> Mark<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>更多热辣资讯尽在新版MSN首页! <a href="http://cn.msn.com/">立刻访问!</a><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>