[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input
gmx3 at hotmail.com
Thu Jan 7 13:03:54 CET 2010
Can you file a bugzilla and attach the tpr file?
> Date: Tue, 5 Jan 2010 10:49:46 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] particle decomposition requires preliminary trjconv -pbc mol input
> Thanks Berk, I actually did not have continuation = yes. I still use
> old-style .mdp options unconstrainted_start and gen_vel (see below),
> although these get replaced by grompp.
> Quoting grompp:
> "Replacing old mdp entry 'unconstrained_start' by 'continuation'"
> gpc-f101n084-$ grep continuation mdout.mdp
> ; For exact run continuation or redoing part of a run
> continuation = no
> Here is my entire .mdp file. I have tested after turning off the pull
> code and it makes no difference.
> gpc-f101n084-$ cat md.mdp
> constraints = all-bonds
> lincs-iter = 1
> lincs-order = 6
> constraint_algorithm = lincs
> integrator = sd
> dt = 0.004
> tinit = 0
> nsteps = 2500
> nstcomm = 1
> nstxout = 250000000
> nstvout = 250000000
> nstfout = 250000000
> nstxtcout = 2500
> nstenergy = 2500
> nstlist = 5
> nstlog=0 ; reduce log file size
> ns_type = grid
> rlist = 1
> rcoulomb = 1
> rvdw = 1
> coulombtype = PME
> ewald-rtol = 1e-5
> optimize_fft = yes
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> tc_grps = System
> tau_t = 1.0
> ld_seed = -1
> ref_t = 300
> gen_temp = 300
> gen_vel = yes
> unconstrained_start = no
> gen_seed = -1
> Pcoupl = berendsen
> pcoupltype = semiisotropic
> tau_p = 4 4
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> ; COM PULLING
> pull = umbrella
> pull_geometry = position
> pull_dim = N N Y
> pull_start = no
> pull_nstxout = 250
> pull_nstfout = 250
> pull_ngroups = 1
> pull_group0 = POPC
> pull_pbcatom0 = 0
> pull_group1 = Protein
> pull_pbcatom1 = 0
> pull_init1 = 0 0 1.32
> pull_rate1 = 0
> pull_k1 = 500.0
> pull_vec1 = 0 0 0
> Thank you,
> --- original message ---
> This should not be a requirement.
> I have not tested this, but from the code it seems this problem can
> only occur when you
> have the mdp option continuation turned on.
> > Date: Sun, 3 Jan 2010 15:53:36 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] particle decomposition requires preliminary
> > trjconv -pbc mol input
> > Hello,
> > I recently used mdrun -pd while attempting to solve my problems with
> > angle_restraints_z
> > (http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html)
> > since I discovered that -noddcheck is not a valid solution to the
> > missing interactions problems with angle restraints.
> > I received immediate errors with particle decomposition (mdrun -pd),
> > although no errors with domain decomposition (mdrun -dd).
> > After a couple of days of changing parameters, I discovered that
> > mdrun -pd requires an input .gro file in which all molecules are
> > whole (as the used to be written out by gromacs mdrun version 3).
> > My basic problem was that I had run parallel EM using domain
> > decomposition and then since my molecules were broken, parallel MD
> > using particle decomposition failed.
> > The solution:
> > grompp -f one.gro -o my.tpr
> > trjconv -s my.tpr -pbc mol -o two.gro
> > grompp -f two.gro -o my.tpr
> > I'm posting so that this can be found by a mailing list search for
> > the next time somebody runs into this as it is, as far as I can
> > tell, an undocumented requirement.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
New Windows 7: Find the right PC for you. Learn more.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users