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

[Berk Hess]

Hi,

There is surely no problem with the gen-pairs option, as that would cause
serious trouble with nearly all simulations performed with Gromacs.

gen-pairs only sets the generation of pair parameters, not of the actual
pair interactions in the topology.

I have no clue to what it going wrong in your system.
You can file a bugzilla at bugzilla.gromacs.org.

Berk

> Date: Mon, 13 Jul 2009 21:09:37 +0200
> From: mikewykes at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA
> 
> 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,
> 
> Mike
> 
> 
> 
> 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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