[gmx-users] Re: Problems with non-bonded interactions using OPLSAA
Mike Wykes
mikewykes at gmail.com
Tue Jul 14 14:21:49 CEST 2009
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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