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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