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

[chris.neale at utoronto.ca]

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.