Hi.
I found the same behavior with both 3 (3.3.3) and 4 (4.0.5) versions on
x86_64.
What I found is :
1. gen-pair correctly generates the 1-4 parameters (verified with
gmxdump -s topol.tpr)
But with no [pairs] defined, 1-4 interactions
are not calculated no matter what the scale factor is.
One has to define the [pairs] to calculate scaled 1-4.
2. It seems that in the case of nrexcl 2 and pairs defined, the 1-4
interactions are calculated twice
(once with scaling 1 in LJ(SR) and once scaled by whatever the
scaling factor is in LJ-14)
With nrexcl 3 and pairs defined only the scaled 1-4 are calculated.
Probably the manual is not clear at this point (p.99 of v4 manual),
where it states :
/The GROMOS force fields list all these interactions explicitly, but
this section might be
empty for force fields like OPLS that calculate the 1-4 interactions by
scaling./
To verify this I did :
zero steps with a single molecule in a large box, varying nrexcl and
scaling factors with pairs defined.
What I found is :
NREXCL SCALE FACTOR LJ(SR) LJ-14
2 0.0 3.22186
0
2 0.5 3.22186
2.58086
2 1.0 3.22186
5.16172
3 0.0 -1.93987
0
3 0.5 -1.93987
2.58086
3 1.0 -1.93987
5.16172
Scaling in 1-4 works as it is expected.
The total LJ (LJ(SR) + LJ-14) in the case of nrexcl 3 and scale factor
1.0 is 3.22185 that is equal to
the LJ(SR) in the case of nrexcl 2 and scale factor 0. This means that
with nrexcl 2,
the 1-4 are calculated unscaled no matter the value of scaling factor
AND scaled by scaling factors,
i.e. scaling 1.5 instead of 0.5 as Mike notes,
Similar for Coulombic interactions.
What I use is nrexcl 3 and pairs defined.
DD
Berk Hess wrote:
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: [email protected]
> To: [email protected]
> 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<[email protected]> 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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