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[求助]
水中溶菌酶教程遇见错误，求指教
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大家好 我是新手 在水中溶菌酶的教程中在第六步平衡中 输入grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -c 后面输入em.gro代表什么意思？ em.gro 能量最小化结构 grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P盲r 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. :-) grompp_mpi (-: Option Filename Type Description ------------------------------------------------------------ -f nvt.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.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 nvt.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file 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.12# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 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... Setting gen_seed to 19890 Velocities were taken from a Maxwell distribution at 300 K 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 Largest charge group radii for Van der Waals: 0.165, 0.156 nm Largest charge group radii for Coulomb: 0.165, 0.164 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 45x45x45, spacing 0.156 0.156 0.156 Estimate for the relative computational load of the PME mesh part: 0.25 This run will generate roughly 399 Mb of data Back Off! I just backed up nvt.tpr to ./#nvt.tpr.5# gcq#133: "You Fill Your Space So Sweet" (F. Apple) 求指教错误原因 |
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