Thanks Berk, this makes sense to me. You were correct that my starting
structure is fully Q+LJ coupled and it is only in the structures where
there is no Q and I then couple LJ to lambda that I get this problem
(and the extension that you suspect). I can just increase rdd. I was
actually using couple-intramol=no, which should "leave on the
intramolecular charge and LJ interactions" from the online manual mdp
options page.
Chris.
-- original message --
Hi,
I think this behavior is "expectable".
The simplest explanation would be that some particles at the ends of
the molecule
only have LJ and no charge, I guess this is not the case.
The more probable explanation is that your molecule extends when the
LJ are turned
off, since there are no interactions to hold it together anymore.
There are two possible solutions:
1. increase -rdd (is by default guessed from the initial structure,
which is probably
compact. Not using domain decomposition completely removed the problem.
2. use couple-intramol to leave on the intramolecular charge and LJ
interactions,
this requires an extra (de-)coupling in vacuum to complete the cycle.
Depending on your system removing or leaving on intramolecular interactions
might lead to more efficient sampling.
Berk
Date: Mon, 6 Apr 2009 18:21:25 -0400
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] missing interactions for the LJ-decoupled
molecule during free energy in parallel but not serial
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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