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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The pull code in Gromacs 3 is pretty messy.<br>The rate is in nm/ps.<br>The force is (unfortunately) not written to the pdo file.<br>You have to redetermine it from the positions,<br>but beware that one of the two groups could jump over the periodic boundary.<br><br>In Gromacs 4 (and the current CVS) I have completely rewritten the pull code.<br></div>There are separate xvg output files with only the positions and only the forces.<br><br>Berk.<br><br><hr id="stopSpelling">> Date: Thu, 14 Aug 2008 08:30:35 +0200<br>> From: malbe@kth.se<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] AFM pulling rate<br>> <br>> Hi,<br>> <br>> The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps.<br>> I have read something in an earlier thread on this list that this might <br>> be a typo, it should be nm/timestep. Does anyone know? I would be happy <br>> if I could have that information.<br>> <br>> Moreover, I am a bit confused about the output in the .pdo-file. In the <br>> description of .pdo-files on page 113 in the manual 3.3.-1 it is <br>> written that the .pdo file will contain calculated forces from <br>> AFM-pulling simulation. On the other hand, on page 118, the description <br>> of the AFM output is that it only contains positions of reference group, <br>> pulled group and spring. This is also the only information I can find in <br>> my output. I wonder if there is a way to get the calculated force into <br>> the pdo file or if it should be done manually (force=k*extension)?<br>> <br>> /Malin Bergenstråhle<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>
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