[gmx-users] table problems

[zhangjianguo2002]

HI everyone,
   I want to make a test using tables potential, I choose full-atoms benzene molecules for example.firstly ,I transform the 12-6 LJ potential into table potential, but when mdrun step, I got a error message as follows:
******************************************************************
Getting Loaded...
Reading file ben_md.tpr, VERSION 3.3.3 (single precision)
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 16534 failed on node n0 (127.0.0.1) due to signal 11.
-----------------------------------------------------------------------------
**************************************************************************
here is my itp and table potential file:
[ defaults ]     
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0
 [ atomtypes ]
;   type      mass    charge    ptype       c6            c12
    BEN        12    0          A           1.00          0.0000
[ moleculetype ]
; Name nrexcl   
BEN      6 
   
[ atoms ]  
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       BEN     1  BEN     C1     1   0  12.0110
     2       BEN     1  BEN     C2     2   0  12.0110
     3       BEN     1  BEN     C3     3   0  12.0110
     4       BEN     1  BEN     C4     4   0  12.0110
     5       BEN     1  BEN     C5     5   0  12.0110
     6       BEN     1  BEN     C6     6   0  12.0110
[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   2    0.139  10800000.0    0.139  10800000.0 ;   CAA  CAB
   2   3   2    0.139  10800000.0    0.139  10800000.0 ;   CAA  CAD
   3   4   2    0.139  10800000.0    0.139  10800000.0 ;   CAB  CAC
   4   5   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAF
   5   6   2    0.139  10800000.0    0.139  10800000.0 ;   CAF  CAE
   6   1   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAD
[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    120.0       505.0    120.0       505.0 ;   HAA  CAA  CAB
   2   3   4   2    120.0       505.0    120.0       505.0 ;   HAA  CAA  CAD
   3   4   5   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  CAD
   4   5   6   2    120.0       505.0    120.0       505.0 ;   CAA  CAB  HAB
   5   6   1   2    120.0       505.0    120.0       505.0 ;   CAA  CAB  CAC
   6   1   2   2    120.0       505.0    120.0       505.0 ;   HAB  CAB  CAC
[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   1   2   3   4   2      0.0  167.4        0.0  167.4   ; imp   CAA  CAD  CAB  HAA
   2   3   4   5   2      0.0  167.4        0.0  167.4   ; imp   CAB  CAA  CAC  HAB
   3   4   5   6   2      0.0  167.4        0.0  167.4   ; imp   CAC  CAB  CAF  HAC
   4   5   6   1   2      0.0  167.4        0.0  167.4   ; imp   CAF  CAC  CAE  HAF
   5   6   1   2   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAF  CAD  HAE
   6   1   2   3   2      0.0  167.4        0.0  167.4   ; imp   CAD  CAA  CAE  HAD
 
part of table potential as follows:
  
    0.36   0  0    0.65757      0     0     0
    0.362  0  0    0.53518      0     0     0
    0.364  0  0    0.42386      0     0     0
    0.366  0  0    0.32271      0     0     0
    0.368  0  0    0.23088      0     0     0
    0.37   0  0    0.14758      0     0     0
    0.372  0  0    0.07213      0     0     0
    0.374  0  0    0.00385      0     0     0
    0.376  0  0    -0.05783     0     0     0
    0.378  0  0    -0.11347     0     0     0
    0.38   0  0    -0.16358     0     0     0
    0.382  0  0    -0.2086      0     0     0
    0.384  0  0    -0.24897     0     0     0
    0.386  0  0    -0.28507     0     0     0
    0.388  0  0    -0.31727     0     0     0
    0.39   0  0    -0.34588     0     0     0
    0.392  0  0    -0.37121     0     0     0
    0.394  0  0    -0.39354     0     0     0
    0.396  0  0    -0.41312     0     0     0
    0.398  0  0    -0.43018     0     0     0
    0.4    0  0    -0.44495     0     0     0
  
*****************************
then ,I change somethings in itp files, add a new type C3,but set its parameters the same as BEN, then em, md ,this time, it words well,but the density of system are 10% less than the full-atom simulation with LJ12-6 potential. I want to know why? table potential can't give the accurate results? another quetion is that, when using tables, if the system has only one type of atoms, Gromas can't work well?
 
 
 changes as follows:
********************************
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0
[ atomtypes ]
;   type      mass    charge    ptype       c6            c12
    BEN        12    0          A           1.00          0.0000
    C3         12    0          A           1.00          0.0000
 [ nonbond_params ]
; i    j         func          c6           c12
 BEN   C3        1             1.00         0.0000
[ moleculetype ]
; Name nrexcl
BEN      6
[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       BEN     1  BEN     C1     1   0  12.0110
     2       BEN     1  BEN     C2     2   0  12.0110
     3       BEN     1  BEN     C3     3   0  12.0110
     4       C3      1  C3     C4     4   0  12.0110
     5       C3      1  C3     C5     5   0  12.0110
     6       C3      1  C3     C6     6   0  12.0110
 *************************
table_BEN_BEN.xvg,table_BEN_C3.xvg,table_BEN_C3.xvg are all the same.
 
Best!
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