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ÎÒÔËÐÐ gromcs,ÏÖÔÚÊÇûÓÐÔ­×ÓÊý²»µÈµÄÎÊÌâÁË£¬µ«ÊÇÓÖ³öÏÖÁËÕâ¸öÎÊÌ⣺
    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      minim.mdp  Input, Opt!  grompp input file with MD parameters
-po      mdout.mdp  Output       grompp input file with MD parameters
  -c      total.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
-rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p        sys.top  Input        Topology file
-pp  processed.top  Output, Opt. Topology file
  -o      input.tpr  Output       Generic run input: tpr tpb tpa xml
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj
  -e       ener.edr  Input, Opt.  Generic energy: 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.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmvsbds   bool    yes  Remove constant bonded interactions with virtual
                            sites
       -load string         Releative load capacity of each node on a
                            parallel machine. Be sure to use quotes around
                            the string, which should contain a number for
                            each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of
                            atomtypes

creating statusfile for 1 node...
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for drg 64
turning H bonds into constraints...
Excluding 2 bonded neighbours for SOL 218
turning H bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
WARNING 1 [file "sys.top", line 37]:
  For minimization with LINCS constraints, lincs_iter should be 4 to 8.
There was 1 warning
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109

Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------

"Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw)
ÎÒµÄsys.topÊÇ£º
;
;       File 'sys.top' was generated
;       By user: zhu (503)
;       On host: apollo2
;       At date: Wed Mar 12 15:48:05 2008
;
;       This is your topology file
;       DRG
;
; Include forcefield parameters
#include "ffG53a6.itp"

; Include surfacetant topology
#include "drg.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
aok in water

[ molecules ]
; Compound        #mols
drg                 64

SOL               218
£¬¶øminim.mdpÎļþΪ£º
; LINES STARTING WITH ';' ARE COMMENTS
title           = Minimization of AOK    ; Title of run

; The following lines tell the program the standard locations where to find cert
ain files
cpp             = /lib/cpp      ; Preprocessor
include         = -I../top      ; Directories to include in the topology format

; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent minimizati
on)
emtol           = 1000.0  ; Stop minimization when the maximum force < 3000.0 kJ
/mol
nsteps          = 100000        ; Maximum number of (minimization) steps to perf
orm
nstenergy       = 10            ; Write energies to disk every nstenergy steps
nstxtcout       = 10            ; Write coordinates to disk every nstxtcout step
s
xtc_grps        = system               ; Which coordinate group(s) to write to d
isk
energygrps      = system               ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to calcul
ate the interactions
nstlist         = 5             ; Frequency to update the neighbor list and long
range forces
ns_type         = simple        ; Method to determine neighbor list (simple, gri
d)
rlist             = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype              = PME  ; Treatment of long range electrostatic interact
ions
rcoulomb                 = 1.0
fourierspacing       =0.12
pme_order            =4
ewald_rtol           =1e-5
optimize_fft         =yes
rvdw            = 1.0           ; long range Van der Waals cut-off
constraints     = hbonds        ; Bond types to replace by constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

;freeze
;freezegrps               = SOL
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ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

boylc789

ľ³æ (ÖøÃûдÊÖ)


¡ï
zyj8119(½ð±Ò+1):лл²ÎÓë
Ìý¹ýÕâ¸öÈí¼þ£¬²»ÖªµÀºÃ²»ºÃʹ
5Â¥2010-12-22 16:58:39
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²é¿´È«²¿ 23 ¸ö»Ø´ð
ÒýÓûØÌû:
Originally posted by zyj8119 at 2010-12-22 14:20:15:
ÎÒÔËÐÐ gromcs,ÏÖÔÚÊÇûÓÐÔ­×ÓÊý²»µÈµÄÎÊÌâÁË£¬µ«ÊÇÓÖ³öÏÖÁËÕâ¸öÎÊÌ⣺
    This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public  ...

ÖØ½ð³êл¡£¡£¡£
2Â¥2010-12-22 15:18:04
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

shengxiang

ľ³æ (ÖøÃûдÊÖ)


¡ï
zyj8119(½ð±Ò+1):лл²ÎÓë
ÒýÓûØÌû:
Originally posted by zyj8119 at 2010-12-22 14:20:15:
ÎÒÔËÐÐ gromcs,ÏÖÔÚÊÇûÓÐÔ­×ÓÊý²»µÈµÄÎÊÌâÁË£¬µ«ÊÇÓÖ³öÏÖÁËÕâ¸öÎÊÌ⣺
    This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public  ...

ÓùýÒ»¶Îʱ¼äµÄGROMACS£¬µ«ÊÇÄãÌáµ½µÄÕâ¸öÎÊÌ⻹ÊǵÚÒ»´ÎÅöµ½¡­¡­ÎÞÄÜΪÁËÁË~
3Â¥2010-12-22 16:10:49
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

mophyworld

½ð³æ (ÕýʽдÊÖ)


¡ï ¡ï ¡ï
zyj8119(½ð±Ò+1):лл²ÎÓë
ghcacj(½ð±Ò+2):лл 2010-12-23 15:52:35
Source code file: grompp.c, line: 1109
Äã¿ÉÒԲ鿴ÏÂÕâÐеĴúÂ룬ÕÒµ½Ô´Í·
4Â¥2010-12-22 16:54:22
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
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matao01114Â¥
2011-01-01 01:09   »Ø¸´  
zyj8119(½ð±Ò+1):лл²ÎÓë
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