[gmx-users] energy group error

[Justin A. Lemkul]

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?
> 

You can't split charge groups, per the error you posted before.

-Justin

> 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
>>
>>   
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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