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Hi,<br><br>I think this behavior is "expectable".<br>The simplest explanation would be that some particles at the ends of the molecule<br>only have LJ and no charge, I guess this is not the case.<br>The more probable explanation is that your molecule extends when the LJ are turned<br>off, since there are no interactions to hold it together anymore.<br>There are two possible solutions:<br>1. increase -rdd (is by default guessed from the initial structure, which is probably<br>compact. Not using domain decomposition completely removed the problem.<br>2. use couple-intramol to leave on the intramolecular charge and LJ interactions,<br>this requires an extra (de-)coupling in vacuum to complete the cycle.<br>Depending on your system removing or leaving on intramolecular interactions<br>might lead to more efficient sampling.<br><br>Berk<br><br>> Date: Mon, 6 Apr 2009 18:21:25 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial<br>> <br>> Hello,<br>> <br>> I am doing free energy calculations with gromacs 4.0.4. For the system I <br>> am using, I have reliable runs without any crashes when running in <br>> serial. When I run in parallel, I get stochastic crashes, that always <br>> have the same form (see below). Note that the "missing interactions" <br>> always involve the decoupled molecule and do not occur when decoupling <br>> the coulombics, but when decoupling the LJ interactions. I have included <br>> error messages below and then the mdp options.<br>> <br>> I will do some more tests to see if I can get rid of the problem by <br>> turning off domain decomposition and whatever else I can think of, but <br>> it strikes me that this may be related to the table representation of <br>> intramolecular interactions for the decoupled molecule not playing nice <br>> with domain decomposition. Any ideas here would be greatly appreciated.<br>> <br>> Thank you,<br>> Chris.<br>> <br>> ########### From the stderr output<br>> <br>> ...<br>> <snip><br>> ...<br>> A list of missing interactions:<br>> LJC Pairs NB of 182 missing 10<br>> exclusions of 86858 missing 10<br>> <br>> Molecule type 'DPN'<br>> the first 10 missing interactions, except for exclusions:<br>> LJC Pairs NB atoms 1 22 global 1 22<br>> LJC Pairs NB atoms 1 23 global 1 23<br>> LJC Pairs NB atoms 2 22 global 2 22<br>> LJC Pairs NB atoms 2 23 global 2 23<br>> LJC Pairs NB atoms 3 22 global 3 22<br>> LJC Pairs NB atoms 3 23 global 3 23<br>> LJC Pairs NB atoms 4 22 global 4 22<br>> LJC Pairs NB atoms 4 23 global 4 23<br>> LJC Pairs NB atoms 5 22 global 5 22<br>> LJC Pairs NB atoms 5 23 global 5 23<br>> <br>> -------------------------------------------------------<br>> Program mdrun_mpi, VERSION 4.0.4<br>> Source code file: domdec_top.c, line: 341<br>> <br>> Fatal error:<br>> 20 of the 104681 bonded interactions could not be calculated because <br>> some atoms involved moved further apart than the multi-body cut-off <br>> distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option <br>> -rdd, for pairs and tabulated bonds also see option -ddcheck<br>> <br>> <br>> ######### And in the .log file:<br>> <br>> ...<br>> <snip><br>> ...<br>> Making 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0<br>> <br>> Center of mass motion removal mode is Linear<br>> We have the following groups for center of mass motion removal:<br>> 0: System<br>> There are: 42663 Atoms<br>> There are: 13807 VSites<br>> Charge group distribution at step 0: 7249 7314<br>> Grid: 15 x 13 x 9 cells<br>> Initial temperature: 304.101 K<br>> <br>> Started mdrun on node 0 Sat Apr 4 09:49:03 2009<br>> <br>> Step Time Lambda<br>> 0 2600.00000 0.94000<br>> <br>> Long Range LJ corr.: <C6> 1.9559e-04<br>> Long Range LJ corr.: Epot -1071.93, Pres: -80.1596, Vir: 1071.93<br>> Energies (kJ/mol)<br>> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br>> 3.06434e+03 7.05100e+02 1.12328e+03 7.39277e+02 6.98859e+03<br>> LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.<br>> 1.00381e+05 -3.08323e+03 -1.07193e+03 -6.15814e+05 -1.04726e+05<br>> COM Pull En. Potential Kinetic En. Total Energy Temperature<br>> 8.31361e-02 -6.11694e+05 1.07966e+05 -5.03728e+05 3.04185e+02<br>> Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd ()<br>> 1.99373e+02 -2.95741e+01 0.00000e+00 0.00000e+00 4.34062e-06<br>> Cons.2 rmsd ()<br>> 4.24190e-06<br>> <br>> DD step 4 load imb.: force 10.3%<br>> <br>> <br>> Not all bonded interactions have been properly assigned to the domain <br>> decomposition cells<br>> <br>> <br>> ########## And the .mdp file:<br>> <br>> ; setup parameters that will be modified by sed during head.sh/sub.sh<br>> nsteps = 50000 ; REMOVE_FOR_EM<br>> tinit = 7600 ; REMOVE_FOR_EM<br>> dt = 0.004 ; REMOVE_FOR_EM<br>> nstxout = 50000 ; REMOVE_FOR_EM<br>> nstvout = 50000 ; REMOVE_FOR_EM<br>> nstfout = 50000 ; REMOVE_FOR_EM<br>> nstenergy = 25000 ; REMOVE_FOR_EM<br>> nstxtcout = 25000 ; REMOVE_FOR_EM<br>> xtc_grps = DPN_DPC ; REMOVE_FOR_EM<br>> nstlog = 250000 ; REMOVE_FOR_EM<br>> gen_vel = no<br>> unconstrained-start = yes<br>> <br>> integrator = sd<br>> energygrps = SOL DPC DPN ; annihilated group must be <br>> separated<br>> gen_seed = -1<br>> comm_mode = linear<br>> nstcomm = 1<br>> comm_grps = System<br>> nstlist = 5<br>> ns_type = grid<br>> pbc = xyz<br>> coulombtype = PME<br>> rcoulomb = 0.9<br>> fourierspacing = 0.12<br>> pme_order = 4<br>> vdwtype = cut-off<br>> rvdw_switch = 0<br>> rvdw = 1.4<br>> rlist = 0.9<br>> DispCorr = EnerPres <br>> Pcoupl = Berendsen ; REMOVE_FOR_EM<br>> pcoupltype = isotropic ; REMOVE_FOR_EM<br>> compressibility = 4.5e-5 ; REMOVE_FOR_EM<br>> ref_p = 1. ; REMOVE_FOR_EM<br>> tau_p = 4.0 ; REMOVE_FOR_EM<br>> tc_grps = System ; REMOVE_FOR_EM<br>> tau_t = 1.0 ; REMOVE_FOR_EM<br>> ld_seed = -1 ; REMOVE_FOR_EM<br>> ref_t = 300. ; REMOVE_FOR_EM<br>> gen_temp = 300. ; REMOVE_FOR_EM<br>> constraints = all-bonds ; REMOVE_FOR_EM<br>> constraint_algorithm= lincs ; REMOVE_FOR_EM<br>> lincs-iter = 1 ; REMOVE_FOR_EM<br>> lincs-order = 6 ; REMOVE_FOR_EM<br>> <br>> ; Free energy control stuff<br>> free_energy = yes<br>> init_lambda = 0.840<br>> delta_lambda = 0<br>> sc-power = 1.0<br>> sc-sigma = 0.3<br>> couple-moltype = DPN<br>> sc_alpha = 0.5<br>> couple-lambda0 = vdw<br>> couple-lambda1 = none<br>> couple-intramol = no<br>> <br>> ;;;Pull groups<br>> pull = umbrella<br>> pull_geometry = distance<br>> pull_dim = Y Y Y<br>> pull_ngroups = 1<br>> pull_group0 = DPC<br>> pull_pbcatom0 = 46<br>> pull_group1 = DPN<br>> pull_k1 = 500<br>> pull_init1 = 1.55<br>> <br>> ;EOF<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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