[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 15 15:12:06 CET 2016 

Hi,

Yes that seems a bit inconsistent. Please file a redmine and include e.g. a
tarball of suitable inputs to reproduce what's going on within grompp.

Mark

On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho <eltonfc at gmail.com> wrote:

> Hi, Mark,
>
> Actually, there seems to be a bug somewhere, because if I defined
> three type 9 dihedrals in a file and then I define the same three type
> 9 dihedrals later on, there should be three warnings: one for each
> multiplicity. there were only two warnings, which means the first one
> somehow is silent.
>
> I just did a quick test and re-enabled the first file. The versions
> #included by forcefield.itp and by the .top file are identical. I get
> two arnings (for multiplicities 2 and 3 like on my first email). If I
> comment out these terms, but keep the first one on the second file, I
> get no warnings by grompp.
>
> This means that grompp reads the three terms from file 1 (hiopefully
> adding them up), then reads a bunch of parameters and then reads the
> first term from file 2, which, according to the documentation (and the
> other warnings) would  throw a warning and overwrite the prvious
> term(s). No warning is given and the user cannot be sure whether the
> term was overriden or added up (depending on where the code branches
> between these alternatives).
>
> Could I file a redmine issue regarding that?
>
>
> On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > Hi,
> >
> > Ok that makes sense. Otherwise it would have seemed like it had to be a
> > code bug.
> >
> > Maybe we could add a warning for including the same file twice? Does
> > anybody do that deliberately E.g with different preprocessor variables
> > defined?
> >
> > Mark
> >
> > On Tue, 15 Nov 2016 00:30 Elton Carvalho <eltonfc at gmail.com> wrote:
> >
> >> My apologies,
> >>
> >> After careful inspection, I noticed that I had #included a copy of
> >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
> >> dihedraltypes ] directive is actually loaded twice, hence the
> >> warnings. Removing the #include from forcefield.itp and keeping it in
> >> the .top file eliminated the warnings and the resulting dynamics seems
> >> sane (read: did not explode).
> >>
> >> Lesson learned: don't change the standard forcefield definition files
> >> when doing preliminary testing. Especially in the end of a 12h layover
> >> between flights.
> >>
> >> Thank you for your attention,
> >> --
> >> Elton
> >>
> >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho <eltonfc at gmail.com>
> wrote:
> >> > Hello, fellow Gromacs Users,
> >> >
> >> > I'm trying to model P3DDT with CGenFF according to the instructions at
> >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
> >> > their website. All this is being done on gromacs 2016.
> >> >
> >> > The script converts the .str file generated by paramchem.org to
> >> > gromacs syntax and units. As a first test, I ran a signle
> >> > dodecylthiophene molecule through the process and obtained apparently
> >> > sane .top and .itp files. The .itp file #includes a .prm file, that
> >> > contains the parameters fitted by the paramchem software.
> >> >
> >> > When running gmx grompp (version 2016), I get these two warnings:
> >> >
> >> > === GROMPP WARNING BEGIN ===
> >> >
> >> > WARNING 1 [file ddt.prm, line 17]:
> >> >   Overriding Proper Dih. parameters.
> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> >> consecutive
> >> >   lines are combined. Non-consective lines overwrite each other.
> >> >
> >> >   old:                                          0 0.8368 1 0 0.8368 1
> >> >   new: CG2R51   CG2R51    CG321    CG321     9     0.000000
> >>  1.129680     2
> >> >
> >> >
> >> > WARNING 2 [file ddt.prm, line 18]:
> >> >   Overriding Proper Dih. parameters.
> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> >> consecutive
> >> >   lines are combined. Non-consective lines overwrite each other.
> >> >
> >> >   old:                                          0 1.12968 2 0 1.12968
> 2
> >> >   new: CG2R51   CG2R51    CG321    CG321     9     0.000000
> >>  0.000000     3
> >> >
> >> > === GROMPP WARNING END ===
> >> >
> >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
> >> > and 18 of the reffered file, as follows:
> >> >
> >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
> >> >
> >> > [ dihedraltypes ]
> >> > ;      i        j        k        l  func         phi0         kphi
> mult
> >> >   CG2R51   CG2R51   CG2R51    CG321     9   180.000000    16.736000
>    2
> >> >    CG321   CG2R51   CG2R51   SG2R50     9   180.000000    29.288000
>    2
> >> >    CG321   CG2R51   CG2R51    HGR51     9   180.000000     4.184000
>    2
> >> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     0.836800
>    1
> >> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     1.129680
>    2
> >> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     0.000000
>    3
> >> >   CG2R51    CG321    CG321    CG321     9     0.000000     0.167360
>    3
> >> >   CG2R51    CG321    CG321     HGA2     9     0.000000     0.836800
>    3
> >> >
> >> > === ddt.prm RELEVANT SECTION END ===
> >> >
> >> > As you can see, the dihedraltype is 9 and the different multiplicities
> >> > of the "CG2R51   CG2R51    CG321    CG321" dihedral are on adjacent
> >> > lines (16, 17 and 18 of the original file. Note that the first warning
> >> > is about overriding the parameters on line 16 with those on line 17,
> >> > so this dihedral is not defined somewhere else).  No wildcard dihedral
> >> > parameters are present in the loaded .itp files.
> >> >
> >> > Why does grompp warn me that it's "Overriding Proper Dih. parameters",
> >> > even though the parameters are entered (to the best of my knowledge)
> >> > as instructed both in the warning and in Section 5.3.3 of the
> >> > Reference Manual? How can I check whether it really did override the
> >> > parameter or added the different terms?
> >> >
> >> > Thanks in advance,
> >> > --
> >> > Elton Carvalho
> >>
> >>
> >>
> >> --
> >> Elton Carvalho
> >> --
> >> Gromacs Users mailing list
> >>
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> > --
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>
> --
> Elton Carvalho
> --
> Gromacs Users mailing list
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