[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

[Berk Hess]

Hi,

Can you file a bugzilla and attach the tpr file?

Thanks,

Berk

> 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,
> Chris.
> 
> --- original message ---
> 
> Hi,
> 
> 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.
> 
> Berk
> 
> > 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.
> 
> 
> -- 
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