Hello,
I am doing free energy calculations with gromacs 4.0.4. For the system I
am using, I have reliable runs without any crashes when running in
serial. When I run in parallel, I get stochastic crashes, that always
have the same form (see below). Note that the "missing interactions"
always involve the decoupled molecule and do not occur when decoupling
the coulombics, but when decoupling the LJ interactions. I have included
error messages below and then the mdp options.
I will do some more tests to see if I can get rid of the problem by
turning off domain decomposition and whatever else I can think of, but
it strikes me that this may be related to the table representation of
intramolecular interactions for the decoupled molecule not playing nice
with domain decomposition. Any ideas here would be greatly appreciated.
Thank you,
Chris.
########### From the stderr output
...
<snip>
...
A list of missing interactions:
LJC Pairs NB of 182 missing 10
exclusions of 86858 missing 10
Molecule type 'DPN'
the first 10 missing interactions, except for exclusions:
LJC Pairs NB atoms 1 22 global 1 22
LJC Pairs NB atoms 1 23 global 1 23
LJC Pairs NB atoms 2 22 global 2 22
LJC Pairs NB atoms 2 23 global 2 23
LJC Pairs NB atoms 3 22 global 3 22
LJC Pairs NB atoms 3 23 global 3 23
LJC Pairs NB atoms 4 22 global 4 22
LJC Pairs NB atoms 4 23 global 4 23
LJC Pairs NB atoms 5 22 global 5 22
LJC Pairs NB atoms 5 23 global 5 23
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_top.c, line: 341
Fatal error:
20 of the 104681 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option
-rdd, for pairs and tabulated bonds also see option -ddcheck
######### And in the .log file:
...
<snip>
...
Making 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: System
There are: 42663 Atoms
There are: 13807 VSites
Charge group distribution at step 0: 7249 7314
Grid: 15 x 13 x 9 cells
Initial temperature: 304.101 K
Started mdrun on node 0 Sat Apr 4 09:49:03 2009
Step Time Lambda
0 2600.00000 0.94000
Long Range LJ corr.: <C6> 1.9559e-04
Long Range LJ corr.: Epot -1071.93, Pres: -80.1596, Vir: 1071.93
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
3.06434e+03 7.05100e+02 1.12328e+03 7.39277e+02 6.98859e+03
LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.
1.00381e+05 -3.08323e+03 -1.07193e+03 -6.15814e+05 -1.04726e+05
COM Pull En. Potential Kinetic En. Total Energy Temperature
8.31361e-02 -6.11694e+05 1.07966e+05 -5.03728e+05 3.04185e+02
Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd ()
1.99373e+02 -2.95741e+01 0.00000e+00 0.00000e+00 4.34062e-06
Cons.2 rmsd ()
4.24190e-06
DD step 4 load imb.: force 10.3%
Not all bonded interactions have been properly assigned to the domain
decomposition cells
########## And the .mdp file:
; setup parameters that will be modified by sed during head.sh/sub.sh
nsteps = 50000 ; REMOVE_FOR_EM
tinit = 7600 ; REMOVE_FOR_EM
dt = 0.004 ; REMOVE_FOR_EM
nstxout = 50000 ; REMOVE_FOR_EM
nstvout = 50000 ; REMOVE_FOR_EM
nstfout = 50000 ; REMOVE_FOR_EM
nstenergy = 25000 ; REMOVE_FOR_EM
nstxtcout = 25000 ; REMOVE_FOR_EM
xtc_grps = DPN_DPC ; REMOVE_FOR_EM
nstlog = 250000 ; REMOVE_FOR_EM
gen_vel = no
unconstrained-start = yes
integrator = sd
energygrps = SOL DPC DPN ; annihilated group must be
separated
gen_seed = -1
comm_mode = linear
nstcomm = 1
comm_grps = System
nstlist = 5
ns_type = grid
pbc = xyz
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
vdwtype = cut-off
rvdw_switch = 0
rvdw = 1.4
rlist = 0.9
DispCorr = EnerPres
Pcoupl = Berendsen ; REMOVE_FOR_EM
pcoupltype = isotropic ; REMOVE_FOR_EM
compressibility = 4.5e-5 ; REMOVE_FOR_EM
ref_p = 1. ; REMOVE_FOR_EM
tau_p = 4.0 ; REMOVE_FOR_EM
tc_grps = System ; REMOVE_FOR_EM
tau_t = 1.0 ; REMOVE_FOR_EM
ld_seed = -1 ; REMOVE_FOR_EM
ref_t = 300. ; REMOVE_FOR_EM
gen_temp = 300. ; REMOVE_FOR_EM
constraints = all-bonds ; REMOVE_FOR_EM
constraint_algorithm= lincs ; REMOVE_FOR_EM
lincs-iter = 1 ; REMOVE_FOR_EM
lincs-order = 6 ; REMOVE_FOR_EM
; Free energy control stuff
free_energy = yes
init_lambda = 0.840
delta_lambda = 0
sc-power = 1.0
sc-sigma = 0.3
couple-moltype = DPN
sc_alpha = 0.5
couple-lambda0 = vdw
couple-lambda1 = none
couple-intramol = no
;;;Pull groups
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_ngroups = 1
pull_group0 = DPC
pull_pbcatom0 = 46
pull_group1 = DPN
pull_k1 = 500
pull_init1 = 1.55
;EOF
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