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虫号: 4116003
注册: 2015-10-02
性别: GG
专业: 合成药物化学

[求助] 用gromacs进行粗粒化操作过程出现问题，求大家帮忙看看

出现“段错误”执行以下操作后出现：
wbs@brisk-wbs:~/design/test1$ mdrun -deffnm equilibration -v
                     :-)  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.

                              :-)  mdrun  (-:

Option    Filename  Type       Description
------------------------------------------------------------
  -s equilibration.tpr  Input       Run input file: tpr tpb tpa
  -o equilibration.trr  Output    Full precision trajectory: trr trj cpt
  -x equilibration.xtc  Output, Opt. Compressed trajectory (portable xdr
                                 format)
-cpi equilibration.cpt  Input, Opt.  Checkpoint file
-cpo equilibration.cpt  Output, Opt. Checkpoint file
  -c equilibration.gro  Output    Structure file: gro g96 pdb etc.
  -e equilibration.edr  Output    Energy file
  -g equilibration.log  Output    Log file
-dhdl equilibration.xvg  Output, Opt. xvgr/xmgr file
-field equilibration.xvg  Output, Opt. xvgr/xmgr file
-table equilibration.xvg  Input, Opt.  xvgr/xmgr file
-tabletf equilibration.xvg  Input, Opt.  xvgr/xmgr file
-tablep equilibration.xvg  Input, Opt.  xvgr/xmgr file
-tableb equilibration.xvg  Input, Opt.  xvgr/xmgr file
-rerun equilibration.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi equilibration.xvg  Output, Opt. xvgr/xmgr file
-tpid equilibration.xvg  Output, Opt. xvgr/xmgr file
-ei equilibration.edi  Input, Opt.  ED sampling input
-eo equilibration.xvg  Output, Opt. xvgr/xmgr file
  -j equilibration.gct  Input, Opt.  General coupling stuff
-jo equilibration.gct  Output, Opt. General coupling stuff
-ffout equilibration.xvg  Output, Opt. xvgr/xmgr file
-devout equilibration.xvg  Output, Opt. xvgr/xmgr file
-runav equilibration.xvg  Output, Opt. xvgr/xmgr file
-px equilibration.xvg  Output, Opt. xvgr/xmgr file
-pf equilibration.xvg  Output, Opt. xvgr/xmgr file
-ro equilibration.xvg  Output, Opt. xvgr/xmgr file
-ra equilibration.log  Output, Opt. Log file
-rs equilibration.log  Output, Opt. Log file
-rt equilibration.log  Output, Opt. Log file
-mtx equilibration.mtx  Output, Opt. Hessian matrix
-dn equilibration.ndx  Output, Opt. Index file
-multidir  equilibration  Input, Opt., Mult. Run directory
-membed equilibration.dat  Input, Opt.  Generic data file
-mp equilibration.top  Input, Opt.  Topology file
-mn equilibration.ndx  Input, Opt.  Index 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
-deffnm    string equilibration  Set the default filename for all file
                        options
-xvg       enum xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd    bool no    Use particle decompostion
-dd       vector 0 0 0 Domain decomposition grid, 0 is optimize
-ddorder    enum interleave  DD node order: interleave, pp_pme or cartesian
-npme       int -1    Number of separate nodes to be used for PME, -1
                        is guess
-nt       int 0    Total number of threads to start (0 is guess)
-ntmpi    int 0    Number of thread-MPI threads to start (0 is guess)
-ntomp    int 0    Number of OpenMP threads per MPI process/thread
                        to start (0 is guess)
-ntomp_pme int 0    Number of OpenMP threads per MPI process/thread
                        to start (0 is -ntomp)
-pin       enum auto Fix threads (or processes) to specific cores:
                        auto, on or off
-pinoffset int 0    The starting logical core number for pinning to
                        cores; used to avoid pinning threads from
                        different mdrun instances to the same core
-pinstride int 0    Pinning distance in logical cores for threads,
                        use 0 to minimize the number of threads per
                        physical core
-gpu_id    string       List of GPU device id-s to use, specifies the
                        per-node PP rank to GPU mapping
-[no]ddcheck bool yes    Check for all bonded interactions with DD
-rdd       real 0    The maximum distance for bonded interactions with
                        DD (nm), 0 is determine from initial coordinates
-rcon       real 0    Maximum distance for P-LINCS (nm), 0 is estimate
-dlb       enum auto Dynamic load balancing (with DD): auto, no or yes
-dds       real 0.8    Minimum allowed dlb scaling of the DD cell size
-gcom       int -1    Global communication frequency
-nb       enum auto Calculate non-bonded interactions on: auto, cpu,
                        gpu or gpu_cpu
-[no]tunepme bool yes    Optimize PME load between PP/PME nodes or GPU/CPU
-[no]testverlet bool no    Test the Verlet non-bonded scheme
-[no]v    bool yes    Be loud and noisy
-[no]compact bool yes    Write a compact log file
-[no]seppot  bool no    Write separate V and dVdl terms for each
                        interaction type and node to the log file(s)
-pforce    real -1    Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool no    Try to avoid optimizations that affect binary
                        reproducibility
-cpt       real 15    Checkpoint interval (minutes)
-[no]cpnum bool no    Keep and number checkpoint files
-[no]append  bool yes    Append to previous output files when continuing
                        from checkpoint instead of adding the simulation
                        part number to all file names
-nsteps    step -2    Run this number of steps, overrides .mdp file
                        option
-maxh       real -1    Terminate after 0.99 times this time (hours)
-multi    int 0    Do multiple simulations in parallel
-replex    int 0    Attempt replica exchange periodically with this
                        period (steps)
-nex       int 0    Number of random exchanges to carry out each
                        exchange interval (N^3 is one suggestion).  -nex
                        zero or not specified gives neighbor replica
                        exchange.
-reseed    int -1    Seed for replica exchange, -1 is generate a seed
-[no]ionize  bool no    Do a simulation including the effect of an X-Ray
                        bombardment on your system

Reading file equilibration.tpr, VERSION 4.6.5 (single precision)
Using 2 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better)
starting mdrun \'Martini system from melittin.pdb\'
25000 steps, 500.0 ps.
step 0Segmentation fault (core dumped)
我在5.X上面也是做到这一里出问题。不知是什么问题。
我是模仿粗粒化教程http://md.chem.rug.nl/index.php/ ... troduction/proteins这里进行操作的。进行官网教程并没有问，应该是
我的文件有问题，不懂怎么修改，出现的note我都忽略了。