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Hi,<br><br>Can you file a bugzilla and attach the tpr file?<br><br>Thanks,<br><br>Berk<br><br>> Date: Tue, 5 Jan 2010 10:49:46 -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>> Thanks Berk, I actually did not have continuation = yes. I still use <br>> old-style .mdp options unconstrainted_start and gen_vel (see below), <br>> although these get replaced by grompp.<br>> <br>> Quoting grompp:<br>> "Replacing old mdp entry 'unconstrained_start' by 'continuation'"<br>> <br>> gpc-f101n084-$ grep continuation mdout.mdp<br>> ; For exact run continuation or redoing part of a run<br>> continuation = no<br>> <br>> ########<br>> <br>> Here is my entire .mdp file. I have tested after turning off the pull <br>> code and it makes no difference.<br>> <br>> gpc-f101n084-$ cat md.mdp<br>> constraints = all-bonds<br>> lincs-iter = 1<br>> lincs-order = 6<br>> constraint_algorithm = lincs<br>> integrator = sd<br>> dt = 0.004<br>> tinit = 0<br>> nsteps = 2500<br>> nstcomm = 1<br>> nstxout = 250000000<br>> nstvout = 250000000<br>> nstfout = 250000000<br>> nstxtcout = 2500<br>> nstenergy = 2500<br>> nstlist = 5<br>> nstlog=0 ; reduce log file size<br>> ns_type = grid<br>> rlist = 1<br>> rcoulomb = 1<br>> rvdw = 1<br>> coulombtype = PME<br>> ewald-rtol = 1e-5<br>> optimize_fft = yes<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4<br>> tc_grps = System<br>> tau_t = 1.0<br>> ld_seed = -1<br>> ref_t = 300<br>> gen_temp = 300<br>> gen_vel = yes<br>> unconstrained_start = no<br>> gen_seed = -1<br>> Pcoupl = berendsen<br>> pcoupltype = semiisotropic<br>> tau_p = 4 4<br>> compressibility = 4.5e-5 4.5e-5<br>> ref_p = 1.0 1.0<br>> <br>> ; COM PULLING<br>> pull = umbrella<br>> pull_geometry = position<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_nstxout = 250<br>> pull_nstfout = 250<br>> pull_ngroups = 1<br>> pull_group0 = POPC<br>> pull_pbcatom0 = 0<br>> pull_group1 = Protein<br>> pull_pbcatom1 = 0<br>> pull_init1 = 0 0 1.32<br>> pull_rate1 = 0<br>> pull_k1 = 500.0<br>> pull_vec1 = 0 0 0<br>> <br>> Thank you,<br>> Chris.<br>> <br>> --- original message ---<br>> <br>> Hi,<br>> <br>> This should not be a requirement.<br>> I have not tested this, but from the code it seems this problem can <br>> 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 at utoronto.ca<br>> > To: gmx-users at gromacs.org<br>> > Subject: [gmx-users] particle decomposition requires preliminary <br>> > 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) <br>> > since I discovered that -noddcheck is not a valid solution to the <br>> > missing 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 <br>> > mdrun -pd requires an input .gro file in which all molecules are <br>> > whole (as 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 <br>> > the next time somebody runs into this as it is, as far as I can <br>> > tell, an undocumented requirement.<br>> <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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