[gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial
Berk Hess
gmx3 at hotmail.com
Tue Apr 7 07:57:51 CEST 2009
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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