[gmx-users] Missing LJ interaction

[Steve Fiedler]

David van der Spoel wrote:
> Steve Fiedler wrote:
>> Thank you for looking over the input and for suggestions Mark.  
>> Unfortunately, a comparison of the topologies with diff revealed no 
>> inconsistencies.  GROMACS can correctly recognize the presence of the 
>> significant repulsion (e+10) between atoms 1 and 5 when the atoms 
>> from both triatomic molecules are incorporated into a single molecule.
>>
>> I have found one clue in that the missing repulsion in the 
>> bimolecular system, can be returned by increasing rlist >= 0.77 nm in 
>> grompp.mdp.  This is unsatisfying, as the distance between atoms 1 
>> and 5 is much shorter, 0.057 nm.  As these coordinates were taken 
>> from a calculation of membrane system just before a crash, I believe 
>> it is this lack of intermolecular nonbonding repulsion responsible 
>> for allowing atoms 1 and 5 to get this close in the first place.
>>
>> Again, any insights are most welcome.
>>
>> Steve
>
> I didn't follow the thread but it is the distance between charge 
> groups that determines whether interactions are incorporated in the 
> neighborlist. Check the manual about charge groups.
>
This issue has been resolved.  Thank you Prof. van der Spoel for 
providing direction.  Below is the corrected topology file of the 
original bimolecular system.  From the mailing list archive, the 
following messages were helpful:

http://www.gromacs.org/pipermail/gmx-users/2003-May/005472.html
http://www.gromacs.org/pipermail/gmx-users/2006-June/022527.html

Thanks again,

Steve

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1     2     no      0.125  0.5

[ atomtypes ]
;name     mass     charge ptype  sig           eps
   C2    14.0300    0.300  A     0.39057      0.49371
   C3    15.0300    0.400  A     0.39057      0.73220
    O    16.0000   -0.694  A     0.30647      0.71128

[ nonbond_params ]
  ; i    j    func    sig          eps
   C2    C2     1     0.39057    0.493712000
   C2    C3     1     0.39057    0.601240800
   C3    C3     1     0.39057    0.732200000
   C2     O     1     0.34852    0.592579920
   C3     O     1     0.34852    0.721656320
    O     O     1     0.30647    0.711280000

[ moleculetype ]
ACHO 1

[ atoms ]
;   nr   type  resnr residue  atom   cgnr  charge       mass
    1     C2    1      1CHO   C2     0      0.000     14.03
    2     C3    1      1CHO   C3     1      0.000     15.03
    3      O    1      1CHO    O     2      0.000     16.00

[ system ]
; name
Two molecules

[ molecules ]
; name   number
ACHO      2

-- 
Steve Fiedler, Ph.D.
Research Fellow
Department of Mechanical Engineering
The University of Michigan
2024 G.G. Brown
2350 Hayward St.
Ann Arbor, MI 48109-2125