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Hi,<br><br>This should not be a requirement.<br>I have not tested this, but from the code it seems this problem can only occur when you<br>have the mdp option continuation turned on.<br><br>Berk<br><br>> Date: Sun, 3 Jan 2010 15:53:36 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] particle decomposition requires preliminary trjconv        -pbc mol input<br>> <br>> Hello,<br>> <br>> I recently used mdrun -pd while attempting to solve my problems with <br>> angle_restraints_z <br>> (http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html) since <br>> I discovered that -noddcheck is not a valid solution to the missing <br>> interactions problems with angle restraints.<br>> <br>> I received immediate errors with particle decomposition (mdrun -pd), <br>> although no errors with domain decomposition (mdrun -dd).<br>> <br>> After a couple of days of changing parameters, I discovered that mdrun <br>> -pd requires an input .gro file in which all molecules are whole (as <br>> the used to be written out by gromacs mdrun version 3).<br>> <br>> My basic problem was that I had run parallel EM using domain <br>> decomposition and then since my molecules were broken, parallel MD <br>> using particle decomposition failed.<br>> <br>> The solution:<br>> grompp -f one.gro -o my.tpr<br>> trjconv -s my.tpr -pbc mol -o two.gro<br>> grompp -f two.gro -o my.tpr<br>> <br>> I'm posting so that this can be found by a mailing list search for the <br>> next time somebody runs into this as it is, as far as I can tell, an <br>> undocumented requirement.<br>> <br>> Chris.<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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