[gmx-users] umbrella sampling tutorial

[Ming Tang]

Dear all,

I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but failed.

; Pull code in tutorial
pull            = umbrella
pull_geometry   = distance      ; simple distance increase
pull_dim        = N N Y
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000          ; kJ mol^-1 nm^-2

; COM pulling I modified
pull            = umbrella
pull_geometry        = distance  ; simple distance increase
pull_dim             = N N Y
pull_start           = yes       ; define initial COM distance > 0
pull_coord1-groups   = 2
pull-group1-name     = Chain_B
pull_group2-name     = Chain_A
pull-coord1-rate     = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k        = 1000      ; kJ mol^-1 nm^-2

Fatal error:
Group Chain_B referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

Index:
[ r_1-27 ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
 121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
 136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
 151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
 166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
 181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
 196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
 211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
 226
[ r_28-54 ]
227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
 242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
 257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
 272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
 287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
 302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
 317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
 332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
 347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
 362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
 377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
 392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
 407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
 422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
 437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
 452

Could anybody tell me what's wrong with the COM pulling code I modified?

Thanks in advance!

Regards,