On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He <xxia...@ust.hk> wrote: > Dear all, > I'm doing an "slow-growth" alchemical free energy perturbation calculation > of the formation of a disulfide bridge between two Cysteines with Gromacs. > I've had tried different ways to combine the topology of both state A and > state B, and finally settled with the most direct way -- to "mutate" the > atoms that have different partial charges in the two states, and transform > the two hydrogen atoms into "dummy" atoms. As suggested by Gromacs manual > and some messages from the internet, I put explicitly the OPLS parameters > for the bonds, pairs, angles and dihedrals changed from state A to state B, > and the grompp didn't give a warning. But when I was testing the production > simulation on two processors, there was a warning of fatal error in the log > file: > ========================================================================================= > Initializing Domain Decomposition on 2 nodes > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: > two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205 > multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417 > Minimum cell size due to bonded interactions: 4.151 nm > Using 0 separate PME nodes > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm > The maximum allowed number of cells is: X 0 Y 0 Z 0 > ------------------------------------------------------- > Program mdrun, VERSION 4.5.4 > Source code file: domdec.c, line: 6436 > Fatal error: > There is no domain decomposition for 2 nodes that is compatible with the > given box and a minimum cell size of 5.18876 nm > Change the number of nodes or mdrun option -rdd or -dds
as suggested by the log: 1] Change the number of nodes or 2] mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ============================================================================================= > The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12 > respectively. I checked the topology and found no entries containing both > these atoms. What's weird is that there's no way for these two atoms to have > bonded interactions, but it says in the log that they have a two-body bonded > interaction with a distance of 3.774 nm, which I cannot understand. > Does anyone have an explanation what this could mean? Any suggestion is > appreciated! > Thanks in advance! > > Xiaoxiao He > Oct. 15, 2011 > > > Attached are the input parameters for the production md: > ===================================================================== > -Input Parameters: > integrator = sd > nsteps = 2000000 > init_step = 0 > ns_type = Grid > nstlist = 10 > ndelta = 2 > nstcomm = 10 > comm_mode = Linear > nstlog = 100 > nstxout = 100000 > nstvout = 100000 > nstfout = 100000 > nstcalcenergy = 10 > nstenergy = 100 > nstxtcout = 1000 > init_t = 0 > delta_t = 0.0005 > xtcprec = 1000 > nkx = 36 > nky = 36 > nkz = 36 > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 0 > epsilon_surface = 0 > optimize_fft = TRUE > ePBC = xyz > bPeriodicMols = FALSE > bContinuation = FALSE > bShakeSOR = FALSE > etc = No > nsttcouple = -1 > epc = Berendsen > epctype = Isotropic > nstpcouple = 10 > tau_p = 1 > ref_p (3x3): > ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} > ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} > ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} > compress (3x3): > compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} > compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} > compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} > refcoord_scaling = No > posres_com (3): > posres_com[0]= 0.00000e+00 > posres_com[1]= 0.00000e+00 > posres_com[2]= 0.00000e+00 > posres_comB (3): > posres_comB[0]= 0.00000e+00 > posres_comB[1]= 0.00000e+00 > posres_comB[2]= 0.00000e+00 > andersen_seed = 815131 > rlist = 1.3 > rlistlong = 1.3 > rtpi = 0.05 > coulombtype = PME > rcoulomb_switch = 0 > rcoulomb = 1.3 > vdwtype = Switch > rvdw_switch = 0.8 > rvdw = 0.9 > epsilon_r = 1 > epsilon_rf = 1 > tabext = 1 > implicit_solvent = No > gb_algorithm = Still > gb_epsilon_solvent = 80 > nstgbradii = 1 > rgbradii = 1 > gb_saltconc = 0 > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Ace-approximation > sa_surface_tension = 2.05016 > DispCorr = EnerPres > free_energy = yes > init_lambda = 0 > delta_lambda = 5e-07 > n_foreign_lambda = 0 > sc_alpha = 0.5 > sc_power = 1 > sc_sigma = 0.3 > sc_sigma_min = 0.3 > nstdhdl = 10 > separate_dhdl_file = no > dhdl_derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > nwall = 0 > wall_type = 9-3 > wall_atomtype[0] = -1 > wall_atomtype[1] = -1 > wall_density[0] = 0 > wall_density[1] = 0 > wall_ewald_zfac = 3 > pull = no > disre = No > disre_weighting = Conservative > disre_mixed = FALSE > dr_fc = 1000 > dr_tau = 0 > nstdisreout = 100 > orires_fc = 0 > orires_tau = 0 > nstorireout = 100 > dihre-fc = 1000 > em_stepsize = 0.01 > em_tol = 10 > niter = 20 > fc_stepsize = 0 > nstcgsteep = 1000 > nbfgscorr = 10 > ConstAlg = Lincs > shake_tol = 0.0001 > lincs_order = 4 > lincs_warnangle = 30 > lincs_iter = 1 > bd_fric = 0 > ld_seed = 1993 > cos_accel = 0 > deform (3x3): > deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > grpopts: > nrdf: 3903 22866 > ref_t: 300 300 > tau_t: 0.1 0.1 > anneal: No No > ann_npoints: 0 0 > acc: 0 0 0 > nfreeze: N N N > energygrp_flags[ 0]: 0 > efield-x: > n = 0 > efield-xt: > n = 0 > efield-y: > n = 0 > efield-yt: > n = 0 > efield-z: > n = 0 > efield-zt: > n = 0 > bQMMM = FALSE > QMconstraints = 0 > QMMMscheme = 0 > scalefactor = 1 > qm_opts: > ngQM = 0 > ====================================================================================================== > > -- > Xiaoxiao HE > Department of Chemistry > The Hong Kong University of Science and Technology > Clear Water Bay, Kowloon > Hong Kong > Email: xxia...@ust.hk Tel: 23585896 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists