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s6120610021

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[求助] 水中溶菌酶教程遇见错误，求指教

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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1楼 2013-01-17 21:31:04

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jiaoyixiong

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感谢参与，应助指数 +1
chaizhm: 金币+2, 谢谢~ 2013-01-18 07:28:16
s6120610021: 金币+2 2013-01-18 09:47:39

手也太新了点儿；遇到问题第一步先看手册，手册上的解释比任何人都权威和详细。

PS，貌似你的log文件没有贴全，出错信息就在log文件最后，或者在你运行的窗口的最下面

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2楼2013-01-17 22:08:12

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s6120610021

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引用回帖:

2楼: Originally posted by jiaoyixiong at 2013-01-17 22:08:12
手也太新了点儿；遇到问题第一步先看手册，手册上的解释比任何人都权威和详细。

PS，貌似你的log文件没有贴全，出错信息就在log文件最后，或者在你运行的窗口的最下面

那个手册在哪里能找到呀，谢谢
这就是全部了 Back Off! I just backed up nvt.tpr to ./#nvt.tpr.5#

gcq#133: "You Fill Your Space So Sweet" (F. Apple)这个地方不是错误的地方么？

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3楼2013-01-18 09:47:09

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jiaoyixiong

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引用回帖:

3楼: Originally posted by s6120610021 at 2013-01-18 09:47:09
那个手册在哪里能找到呀，谢谢
这就是全部了 Back Off! I just backed up nvt.tpr to ./#nvt.tpr.5#

gcq#133: "You Fill Your Space So Sweet" (F. Apple)这个地方不是错误的地方么？...

如果你的 log文件最后就显示这些内容，那应该就是在算，如果出错，就有错误提示的。

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4楼2013-01-18 11:25:08

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