[交流] 【求助】gromacs的一個新問題

版本問題算是解決了，但是又遇到一個新問題：
zyj@zyj-laptop:~/桌面/drg$ grompp -f fullmd.mdp -c minimized_water.gro -p sys.to
p -o fullmd.tpr
                     :-)  G  R  O  M  A  C  S  (-:

            GROningen Mixture of Alchemy and Childrens' Stories

                        :-)  VERSION 4.0.7  (-:

   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
         Copyright (c) 2001-2008, The GROMACS development team,
         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  (-:

Option    Filename  Type       Description
------------------------------------------------------------
  -f    fullmd.mdp  Input, Opt!  grompp input file with MD parameters
-po    mdout.mdp  Output    grompp input file with MD parameters
  -c minimized_water.gro  Input       Structure file: gro g96 pdb tpr tpb tpa
  -r    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
-rb    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n    index.ndx  Input, Opt.  Index file
  -p       sys.top  Input       Topology file
-pp  processed.top  Output, Opt. Topology file
  -o    fullmd.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: edr ene

Option    Type Value Description
------------------------------------------------------
-[no]h    bool no    Print help info and quit
-nice       int 0    Set the nicelevel
-[no]v    bool yes    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
-[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'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...

NOTE 1 [file fullmd.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

processing topology...
Opening library file /usr/share/gromacs/top/ffG53a6.itp
Opening library file /usr/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /usr/share/gromacs/top/spce.itp
Opening library file /usr/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'DRG'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 290 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 46055    OTHER residues
There are:    0 PROTEIN residues
There are:    0       DNA residues
Analysing Other...

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/readir.c, line: 1069

Fatal error:
137973 atoms are not part of any of the T-Coupling groups
-------------------------------------------------------

"Look at these, my work-strong arms" (P.J. Harvey)

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1樓 2011-01-07 18:00:51

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zyj8119

木蟲 (著名寫手)

引用回帖:

Originally posted by zyj8119 at 2011-01-07 18:02:24:

zyj@zyj-laptop:~/桌面/drg$ ls
drg.gro    md.log       minimized_box.gro minim_traj.trr  #sys.top.1#
drg.itp    mdout.mdp    minimized.gro       out.gro
fullmd.mdp  #mdout.mdp.1# ...

此問題也解決了，是temperature coupling的問題。

贊一下

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3樓2011-01-07 23:17:58

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zyj8119

木蟲 (著名寫手)

引用回帖:

Originally posted by zyj8119 at 2011-01-07 18:00:51:
版本問題算是解決了，但是又遇到一個新問題：
zyj@zyj-laptop:~/桌面/drg$ grompp -f fullmd.mdp -c minimized_water.gro -p sys.to
p -o fullmd.tpr
:-) G R O M A C S (-: ...

zyj@zyj-laptop:~/桌面/drg$ ls
drg.gro    md.log       minimized_box.gro minim_traj.trr  #sys.top.1#
drg.itp    mdout.mdp    minimized.gro       out.gro
fullmd.mdp  #mdout.mdp.1# minimized_water.gro  sys.top
input.tpr minim_ener.edr  minim.mdp          sys.top~

贊一下

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2樓2011-01-07 18:02:24

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