[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Elton Carvalho
eltonfc at gmail.com
Tue Nov 15 19:35:43 CET 2016
Issue #2077 created, thanks!
On Tue, Nov 15, 2016 at 11:11 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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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