[gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Mike Wykes mikewykes at gmail.com
Mon Jul 13 21:09:37 CEST 2009

Dear all

I have since found the problem. For some reason gen-pairs = yes option
is not working, so my 1-4 interactions were being completely excluded
and not scaled by 0.5 as they should have been. Defining all 1-4 pairs
in a [ pairs ] section in conjunction with nexcl =3 in the topology
solved the problem.

I was not sure whether to use nexcl =2 or nexcl =3 in the case of
scaled 1-4 interactions, but by trial and error I found that one
should use nexcl =3, otherwise you have the full 1-4 interaction + the
scaled one, so in total a scaling of 1.5 instead of 0.5.

Any ideas why gen-pairs = yes option is not working would be much appreciated.

Thanks to those who responded to my first email,


On Thu, Jul 2, 2009 at 6:54 PM, Mike Wykes<mikewykes at gmail.com> wrote:
> Dear all
>  I would like to simulate beta cyclodextrin in various organic
> solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18:
> 1955-1970, 1997) but am having problems with the short range Coulomb
> and LJ interactions.
> This FF (and OPLS in general) does not assign LJ parameters to
> hydrogen atoms in OH groups, relying on the repulsion between oxygens
> to keep the hydrogen (charge +0.435 ) of one OH group getting too
> close to the O (charge -0.7 ) of another.
> However in MD simulations, the hydrogen of one OH group collides with
> the O of another, and shortly after the system explodes.
> Obviously, this could be a mistake of how I converted the parameters
> in the paper into gromacs parameters, so I have checked this and found
> no mistakes. Some of the parameters are taken from regular OPLS,
> allowing me to check my conversion by comparing to the parameters in
> gromacs/share/top/ffoplsaa*.itp files.
> Out of curiosity I implemented the same forcefield in the tinker md
> package and the O...H system was stable during MD, with no O..H
> collisions. Comparing the energies of exactly the same geometry of
> beta cyclodextrin with the same OPLS parameters shows identical bonded
> interactions, but differences in the non-bonded interactions:
>                     tinker(kcal/mol)   gmx (kj/mol)   gmx(kcal/mol)    difference
> Total   Potential energy 312           -1416.98 -338.67 650.67
>  Bond Stretching        23.32   97.58   23.32   0
> Angle Bending           30.38   127.11  30.38   0
>  Torsional Angle                312.06  1305.64 312.06  0
> Van der Waals           13.69   -119.03 -28.45  42.14
> Charge-Charge           -67.45  -2828.29        -675.98 608.52
> In both cases the molecule was in the gas phase, all non-bonded
> interactions being treated with a cutoff of 1.5 nm.
> Any suggestions as to what could be going wrong in my gromacs
> calculations would be much appreciated.
> Please find my mdp, top and itp files below. I am using version 4.0.5.
> Many thanks,
> Mike

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