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十年磨练木虫 (正式写手)
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gromacs软件中grompp命令运行出现警告已有1人参与
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如题，我在运行《水中的溶菌酶》教程时，出现错误。不知道是什么原因，求大家解答 root@wu-MS-7788:~# grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr :-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------ -f md.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c npt.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o md_0_1.tpr Output Run input file: tpr tpb tpa -t npt.cpt Input, Opt! Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# WARNING 1 [file md.mdp, line 47]: Unknown left-hand 'nstxout-compressed' in parameter file WARNING 2 [file md.mdp, line 47]: Unknown left-hand 'compressed-x-grps' in parameter file Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 129 Protein residues There are: 10824 Water residues There are: 8 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group Protein is 3895.83 Number of degrees of freedom in T-Coupling group non-Protein is 64965.17 Determining Verlet buffer for an energy drift of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.035 nm, buffer size 0.035 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 100.000 Using frame at t = 100 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 44x44x44, spacing 0.159 0.159 0.159 Estimate for the relative computational load of the PME mesh part: 0.16 This run will generate roughly 83 Mb of data There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1910 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Gabba Gabba Hey!" (The Ramones) md.mdp文件参数为： title = OPLS Lysozyme MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; replaces xtc-grps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off |
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