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zyj8119

木虫 (著名写手)

[交流] 【求助】gromacs的又一个问题

我运行 gromcs,现在是没有原子数不等的问题了，但是又出现了这个问题：
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)
我的sys.top是：
;
;    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
，而minim.mdp文件为：
; 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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1楼 2010-12-22 14:20:15

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zyj8119

木虫 (著名写手)

引用回帖:

Originally posted by mophyworld at 2010-12-22 16:54:22:
Source code file: grompp.c, line: 1109
你可以查看下这行的代码，找到源头

static void check_gbsa_params(t_inputrec *ir,gpp_atomtype_t atype)
{
int  nmiss,i;

/* If we are doing GBSA, check that we got the parameters we need
   * This checking is to see if there are GBSA paratmeters for all
   * atoms in the force field. To go around this for testing purposes
   * comment out the nerror++ counter temporarily
   */
nmiss = 0;
for(i=0;i {
      if (get_atomtype_radius(i,atype) < 0 ||
         get_atomtype_vol(i,atype)    < 0 ||
         get_atomtype_surftens(i,atype)  < 0 ||
         get_atomtype_gb_radius(i,atype) < 0 ||
         get_atomtype_S_hct(i,atype)    < 0)
      {
         fprintf(stderr,"\nGB parameter(s) missing or negative for atom type '%s'\n",
                  get_atomtype_name(i,atype));
         nmiss++;
      }
}

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6楼2010-12-22 17:10:30

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zyj8119

木虫 (著名写手)

引用回帖:

Originally posted by zyj8119 at 2010-12-22 14:20:15:
我运行 gromcs,现在是没有原子数不等的问题了，但是又出现了这个问题：
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public ...

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2楼2010-12-22 15:18:04

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