[gmx-users] energy group error

[Gavin Melaugh]

Hi again

To rephrase. If I have two atoms constructing a charge group, is it not
possible to have one of these atoms constructing an energy group on its own?

Cheers

Gavin
Gavin Melaugh wrote:
> Hi All
>
> I have set up a topology file and with virtual sites (exerpts below),
> whereby my virtual sites only interact with the C3 atoms. I am trying to
> construct a PMF wrt one particular C3. This atom I do not want to
> interact with the virtual sites at all. I thought the best way to do
> this was via energy exclusion groups. So I set up some groups in the
> index file (see below), and defined the energy groups like so
> energygrps  = vsites vsitex
> energygrp_excl = vsites vsitex
>
> but I get the following error
>
> Fatal error:
> atoms 415 and 416 in charge group 89 of molecule type 'name' are in
> different energy groups
> I have no charge group 89 in my molecule. Can someone please suggest
> where I might be going wrong.
>
> ;Parameter level
> [defaults]
> ; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
>      1         3              yes            0.5         0.5
>
> [atomtypes]
> ;type     mass           charge      ptype     sigma(nm)    
> epsilon(kjmol-1)
>    CB     12.011000      0.000000       A      0.355000      0.292880
>    CA     12.011000     -0.115000       A      0.355000      0.292880
>    HC      1.008000      0.115000       A      0.242000      0.125520
>    CU     13.019000      0.265000       A      0.350000      0.334720
>    NU     14.007000     -0.597000       A      0.325000      0.711280
>    CH     13.019000      0.332000       A      0.385000      0.334720
>    C3     15.035000      0.000000       A      0.391000      0.669440
>    C2     14.027000      0.000000       A      0.390500      0.493712
>    VS      0.0           0.0            V      0.0           0.0
>
> [nonbond_params]
> ;i  j  funct  sigma  epsilon
> VS  C3  1      0.1    0.03153
>
>
> [ cage_1 ]
>    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   75   89  103  117  131  145  159  173  187  201  215
> [ tail ]
>  416
> [ vsites ]
>  229  230  231  232  461  462  463  464
> [ vsitex ]
>  416
>
>