I am trying to simulate a system with a phosphorylated threonine residue using Gromacs 4.5.5. I took the parameters for the TPO residue from the gromos43a1p force field and added them to the gromos43a1 force field, following the steps as provided on the Gromacs website. I then successfully completed the following steps.
$bin/pdb2gmx -ignh -ff gromos43a1 -f odh.pdb -o odh.pdb -p odh.top -water spce $bin/editconf -bt octahedron -f odh.pdb -o odh-b4sol.pdb -d 1.0 $bin/genbox -cp odh-b4sol.pdb -cs spc216.gro -o odh-b4ion.pdb -p odh.top $bin/grompp -f em.mdp -c odh-b4ion.pdb -p odh.top -o ion.tpr -maxwarn 5 $bin/genion -s ion.tpr -o odh-b4em.pdb -neutral -conc 0.15 -p odh.top -g ion.log $bin/grompp -f em.mdp -c odh-b4em.pdb -p odh.top -o em.tpr -maxwarn 5 I then tried to carry out the energy minimization (the em.mdp file is attached) $bin/mdrun -v -deffnm em Only to encounter the following error Fatal error: 6 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Repeating the command causes different numbers of particles to be included in the error. I have attached a log file from mdrun. I repeated all steps with the same protein except with a THR in place of the TPO and found no errors. The initial structure had been minimized in CHARMM, so I downloaded the original pdb and tested it, only to find the same error. I then tried simulating a single TPO with the same set of steps (the editconf command option -d 1.0 was changed to 5.0) and found the same error. I then tried using the gromos43a1p force field more directly. I used the gromos43a1 .hdb (and added an entry for TPO) and .atp files in place of the the ones found in the gromos43a1p directory because of previously discussed issues with the format. I also added the ions.itp, spce.itp, and ff_dum.itp to the directory. However, after inputting the same commands and using the single TPO residue, I received the same error. Alex Cumberworth
Log file opened on Tue Jun 5 16:13:08 2012 Host: sophie.chibi.ubc.ca pid: 28093 nodeid: 0 nnodes: 1 The Gromacs distribution was built Tue May 15 17:11:59 PDT 2012 by [email protected] (Linux 2.6.18-194.17.4.el5 x86_64) :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /home/alexc/bin/gromacs/bin/mdrun (-: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md nsteps = 400 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm_mode = Linear nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstcalcenergy = 10 nstenergy = 100 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 64 nky = 64 nkz = 64 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 = No epctype = Isotropic nstpcouple = -1 tau_p = 1 ref_p (3x3): ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 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 rlistlong = 1.4 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.4 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 = No free_energy = no init_lambda = 0 delta_lambda = 0 n_foreign_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 sc_sigma_min = 0.3 nstdhdl = 10 separate_dhdl_file = yes 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 = 1000 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: 88230 ref_t: 0 tau_t: 0 anneal: No ann_npoints: 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 Initializing Domain Decomposition on 24 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: 0.586 nm, LJ-14, atoms 1034 1052 multi-body bonded interactions: 0.586 nm, Proper Dih., atoms 1034 1052 Minimum cell size due to bonded interactions: 0.645 nm Guess for relative PME load: 0.33 Will use 16 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 8 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 16 cells with a minimum initial size of 0.806 nm The maximum allowed number of cells is: X 7 Y 7 Z 7 Domain decomposition grid 4 x 4 x 1, separate PME nodes 8 PME domain decomposition: 4 x 2 x 1 Interleaving PP and PME nodes This is a particle-particle only node Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4 System total charge: 0.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC-like water optimization for 9325 molecules. Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Removing pbc first time Linking all bonded interactions to atoms There are 4710 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 1.55 nm Y 1.50 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.400 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 2 The minimum size for domain decomposition cells is 1.045 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.68 Y 0.69 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.045 nm Making 2D domain decomposition grid 4 x 4 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: rest There are: 29411 Atoms Charge group distribution at step 0: 642 617 633 635 650 609 594 628 634 579 616 624 633 633 630 628 Grid: 10 x 10 x 9 cells Initial temperature: 0 K Started mdrun on node 0 Tue Jun 5 16:13:08 2012 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 5.32700e+02 8.46056e+02 6.09061e+01 1.06330e+03 1.02962e+03 Improper Dih. LJ-14 Coulomb-14 LJ (SR) LJ (LR) 6.00495e+01 5.77107e+02 1.50086e+04 3.00573e+05 -1.33813e+03 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -4.42976e+05 -4.81722e+04 -1.72736e+05 1.00506e+07 9.87782e+06 Temperature Pressure (bar) 2.74010e+04 4.34738e+05 ------------------------------------------------------- Program mdrun, VERSION 4.5.5 Source code file: pme.c, line: 538 Fatal error: 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop)
em.mdp
Description: application/mdp
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