[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Elton Carvalho
eltonfc at gmail.com
Tue Nov 15 15:00:56 CET 2016
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
>> --
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