[gmx-users] Re: Problems with non-bonded interactions using OPLSAA
Berk Hess
gmx3 at hotmail.com
Tue Jul 14 14:32:03 CEST 2009
Hi,
I changed that part as well and also updated it for the fact that grompp
in 4.0 never generates zero parameters, but always generates a fatal error
when parameters are missing.
Berk
> Date: Tue, 14 Jul 2009 14:21:49 +0200
> Subject: Re: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA
> From: mikewykes at gmail.com
> To: gmx-users at gromacs.org
>
> Thanks for the clarification, that explains everything.
>
> Perhaps page 112 of the v4 manual could be updated too :
>
> "generate pairs = no (the default, get 1-4 interactions from the pair
> list, when parameters are
> not present in the list give a warning and use zeros) or yes (generate
> 1-4 interactions which
> are not present in the pair list from normal Lennard-Jones parameters
> using FudgeLJ)"
>
> Replacing 'interactions' with 'parameters' would make things clearer here too..
>
> Regards
>
> Mike
>
> On Tue, Jul 14, 2009 at 12:55 PM, Berk Hess<gmx3 at hotmail.com> wrote:
> > Hi,
> >
> > Again, to avoid confusion:
> > there are two (or three) completely separate parts to this issue in Gromacs.
> >
> > 1) The generation of the actual pair interactions in the [ pairs ] section
> > in the topology (.top) file. pdb2gmx does this for you.
> > If you write a topology by hand, you also have to add the 1-4 interactions
> > in the [ pairs ] section by hand.
> >
> > 2) The generation of the interaction parameters for the interactions
> > in the [ pairs ] section. This is what gen-pairs switches and this is what
> > the comment in the manual is about. Pair parameters are taken from
> > the [ pairtypes ] section in the force field file or topology file.
> > If parameters are not found for a certain pair of atom types in [ pairtypes
> > ],
> > they will be generated when gen-pairs is true, a fatal error will be
> > generated when gen-pairs is false.
> > (I will change "interactions" to "interaction parameters" in the quoted
> > line of the manual.)
> >
> > 3) pairs are bonded interactions and bonded interactions in no way affect
> > the calculation of non-bonded interactions in Gromacs. Thus to not calculate
> > interactions twice, you need to use nrexcl=3 when you put 1-4 interactions
> > in the [ pairs ] section.
> >
> > Berk
> >
> > ________________________________
> > Date: Tue, 14 Jul 2009 13:43:19 +0300
> > From: ntelll at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Re: Problems with non-bonded interactions using
> > OPLSAA
> >
> > 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: 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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