[gmx-users] energy group error

[Mark Abraham]

On 05/11/2011 02:04 AM, Gavin Melaugh wrote:
> 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?

Correct. Neighbour lists are constructed from the set of whole charge 
groups in each energy group, as the error suggests.

Mark

> 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
>>
>>