Jamie Seyed wrote:
Hi Justin,
I read the section 4.6.2, so according to the section I should have groups with 0 charge, so I assigned each ch3 (total charge=0) for cgnr

Charge groups, in general, should at least have integer charge (i.e., carboxylate in an ASP side chain), but yes, zero is generally good.

the same number. I still get the same Note. Should I assigned the same

Each CH3 groups should be its own charge group. You should not have multiple CH3 groups in the same charge group.

number for all atoms to cgnr in the atom section of itp-file?? In this way my whole molecule will consider as one group which indeed has a charge=0?? Is this true??

No. You'd be making the problems worse. The note is very clear - charge groups should have very few atoms to avoid cutoff artefacts. If you assign your whole structure to a charge group, you will still get the same note. You have to take a large structure, break it down into smaller pieces of unit charge, and make those your charge groups.

Look at your largest charge group, figure out what's in it, and decompose it into smaller functional groups. Don't make any of them bigger.

-Justin

Thanks a lot/Jamie

On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:



    Jamie Seyed wrote:

        Hi Justin,

        Is there any information on the gmx-website that explains how I
        should do that? Does the tip means I should separate my original
        structure and the groups that I attached to it??/ Many Thanks/Jamie


    Please see the manual, section 4.6.2.  I don't know what you mean by
    separating your structure.

    -Justin

        On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:

           Jamie Seyed wrote: > Dear Justin, > Thanks for your all valuable
           comments. Actually I got these 2 notes: >
-----------------------------------------------------------------------------------
            > > NOTE 1 [file topol.top, line unknown]: > The largest charge
           group contains 24 atoms. > Since atoms only see each other
        when the
           centers of geometry of the charge > groups they belong to are
        within
           the cut-off distance, too large charge > groups can lead to
        serious
           cut-off artifacts. > For efficiency and accuracy, charge group
           should consist of a few atoms. > For all-atom force fields
        use: CH3,
           CH2, CH, NH2, NH, OH, CO2, CO, etc. > > NOTE 2 [file md.mdp, line
           unknown]: > You are using a plain Coulomb cut-off, which might
           produce artifacts. > You might want to consider using PME
           electrostatics. > >
           ------------------------------------------------- > > How I can
           trust my results specially for first one?? Many Thanks/Jamie
         > You
           should define smaller charge groups. The tip given in the note is
           useful. As for note 2, never use cut-off for electrostatics.
        It is
           not as reliable as PME. -Justin > > > On Mon, Aug 10, 2009 at
        9:18
           PM, Justin A. Lemkul > wrote: > > > > Jamie Seyed wrote: > >
        The gro
           file: > ------------------------- > GROtesk MACabre and
        Sinister >
           1836 > 12 C 1 1.311 1.563 0.994 > 12 C 2 1.220 1.635 1.079 >
        12 C 3
           1.092 1.565 1.081 > 12 C 4 1.108 1.449 0.996 > ......... > > 12 H
           118 1.438 1.092 1.244 > 12 H 119 1.413 1.098 1.426 > 12 H 120
        1.291
           1.033 1.329 > 2SOL OW 121 0.569 1.275 1.165 > 2SOL HW1 122 0.476
           1.268 1.128 > 2SOL HW2 123 0.580 1.364 1.209 > > ....... > >
        572SOL
           HW2 1833 2.024 1.991 2.158 > 573SOL OW 1834 2.290 2.286 2.382 >
           573SOL HW1 1835 2.320 2.214 2.320 > 573SOL HW2 1836 2.251 2.246
           2.465 > 2.64467 2.64467 2.64467 > >
           ----------------------------------------- > and itp-file: > >
           ----------------- > > ; Include forcefield parameters > > [
           moleculetype ] > ; Name nrexcl > C60CH3 3 > > [ atoms ] > ;
        nr type
           resnr residue atom cgnr charge > mass typeB chargeB massB > 1
           opls_145 1 C60CH3 C 1 0 > 12.011 ; qtot 0 > 2 opls_516 1
        C60CH3 C 2
           0 > 12.011 ; qtot 0 > ..... > > > 71 78 79 69 3 1.740000e+02
           5.000000e+00 > 3.000000e+00 1.740000e+02 5.000000e+00
        3.000000e+00 >
           69 79 80 2 3 2.580000e+02 5.000000e+00 > 3.000000e+00
        2.580000e+02
           5.000000e+00 3.000000e+00 > > [ system ] > ; Name > C60CH3 > > [
           molecules ] > ; Compound #mols > C60CH3 1 >
           ----------------------------------------------- > > Oh Ok now I
           understand that I should remove only one of the > [molecule]
         > > >
           The [ system ] and [ molecules ] directives *only* belong in
        the >
           system .top, never in an .itp file. Remove both [ system ]
        and [ >
           molecules ] from the .itp, and list the appropriate molecules
        in the
            > [ molecules ] directive of the .top only. > > -Justin > >
           sections in itp-file (right)?? > > Thanks a lot/ Please let
        me know
           if still something is > missing.../Thanks/Jamie > > > On Mon, Aug
           10, 2009 at 8:42 PM, Justin A. Lemkul > > >> wrote: > > > > Jamie
           Seyed wrote: > > First I put 1000, but after editconf and
        genbox it
           has been > changed to 572. I only have 1 part with SOL 572...
         > > >
           I'm thoroughly confused. There is no need to manually
        manipulate >
           these sections if you're allowing genbox, genion, etc to >
           manipulate > them for you. Please post the following
        information to
           get a > resolution: > > 1. Your .top file > 2. Your molecule.itp
           file (you can delete out lines in the atoms, > bonds, dihedrals
           section so the file is not unnecessarily > long - I'm >
        really just
           interested in the other directives that may be > present) > >
           -Justin > > On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul
         > > >
            > > >>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, > >
        Thanks
           again... . Actully I have a question: I > have 1836 > atoms >
        (572
           water and 1 molecule with 120 atoms). In top > of my >
        file.gro > I
           have 1836 and in topology in [molecules] I have > c60ch3 > 1;
        and >
           SOL 572 which means the same as above. So how I should >
        change it >
           to get rid of error...??/ > > > The above should be correct.
           However, you then have > in your .top > you posted earlier: > > >
           [molecules] > molecule 1 > SOL 1000 > > This section is
        probably the
           source of your problem. > Again, as I > said before, there should
           only ever be one [ molecules ] > section in > the .top file.
        Sounds
           like you've got two. > > -Justin > > Thank you in
        advance.../Jamie >
           On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul > > > > >
         >> > > >
            > > >>>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, >
        Oh yes.
           I had a line that include ff again > and I > deleted that >
        (is that
           ok)? now I got a new error related to > "number of >
        coordinates in
            > > > That's more than OK, that's correct. As Mark > pointed
         > out,
           there > should only ever be one invocation of [ > defaults ]
        in > a
           topology. > > > coordinate file does not match topology..." I >
           should fix this > one now!! Simple one to > fix. Figure out where
           the duplicate or > missing > molecules are within the
        topology. I'm
            > guessing your > molecule.itp > was really a molecule.top,
           complete with [ > defaults ], [ > system ], > and [ molecules ]
           directive, right? None of these > should be > present > in an
        .itp
           file, only a .top. > > -Justin > > Thanks a lot/Jamie > > >
        On Mon,
           Aug 10, 2009 at 8:10 PM, Justin A. > Lemkul > > > > > >> > >
         > > >
            >>> > > > > >> > > > > > >>>>> wrote: > > > Can you post the
           contents of > molecule.itp? The > first > #include for > the
        force
           field is likely not the problem; > you've probably >
        #included > it
           again in molecule.itp. > > -Justin > > Jamie Seyed wrote: > >
        Dear
           all, > I have a topology contains line as > below. I > do not >
           understand > what is wrong with it that I get an > error >
           ----------- > Program grompp, Version 4.0.5 > Source Code file:
           topio.c, line: 415 > Fatal error: > Syntax error-File
        ffoplsaa.itp,
           line 18 > last line read: > '[defaults]' > Invalid order for
           directive defaults > -------------- > according to the page > >
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
            > I do not have twice default > section... SO I > do not >
        know >
           exactly > which files I should check... It says > topology
        and ff. >
           Topology > that I am using in grompp is as > below and the >
           ffoplsaa.itp has > only one default section... > Would you please
           help me to solve > the problem. > topol.top: ------------- >
           #include "ffoplsaa.itp" > #include "spce.itp" > #include
           "molecule.itp" > [system] > fullerene in water > [molecules] >
           molecule 1 > SOL 1000 > -------------------- > Many Thanks in
           Advance and I > appreciate your > help/Jamie > > On Mon, Aug 10,
           2009 at 5:46 PM, > Jamie Seyed > > > > > >> > > > > >>> > > >
         > > >>
            > > > > >>>> > > > > >> > > > > > >>> > > > >> > > > > >
         >>>>>> > >
           wrote: > > Dear Vitaly, > topol.top: ------------- > #include
           "ffoplsaa.itp" > #include "spce.itp" > #include "c80ch3.itp" >
           [system] > fullerene in water > [molecules] > C80CH3 1 > SOL
        1000 >
           -------------------- > my command is: > grompp -f md.mdp -c
        f.gro -p
            > topol.top > -o pr.tpr > -maxwarn 10 > Thank you for helping me
           out to > solve the > problem/ > Regards/Jamie > On Mon, Aug
        10, 2009
           at > 5:39 PM, > Vitaly > V. Chaban > > > > > >> > > > > >>> >
         > > >
            > >> > > > > >>>> > > > > >> > > > > >>> > > > > > >> > > > >
            >>>>>> wrote: > > Jamie, > > The idea is the same. Some >
        directive
            > is not > at its > place. I > cannot say > which is exactly
           because I > don't see > all the > picture with > your > topology
           file (+included files). > Write the > sequence of >
        directives as >
           they go in .top (+included > .itp) and > then > we will see >
        what
           sections > must be shifted or maybe just > swapped. > >
        Vitaly > >
           On Tue, Aug 11, 2009 at 12:34 > AM, Jamie > Seyed > > > >> >
         > > >
            >>> > > > > >> > > > > > >>>> > > > > > >> > > > > > >>> > >
         > > >
            >> > > > > > >>>>>> wrote: > > Hi Vitaly, > > When I add it
        back, I
           got > the old > error > > ----------- > > Program grompp, Version
           4.0.5 > > Source Code file: topio.c, > line: 415 > > Fatal
        error: >
            > Syntax error-File > ffoplsaa.itp, > line 18 > > last line
        read: >
            > '[defaults]' > > Invalid order for > directive defaults > >
           ----------- > > Now do you have any idea??? I > appreciate >
        your >
           help/Jamie > > > > On Mon, Aug 10, 2009 at > 5:22 PM, > Jamie
        Seyed
            > > > > >> > > > > > >>> > > > >> > > > > > >>>> > > > > >>
         > > > >
            > >>> > > > >> > > > > > >>>>>> > > wrote: > >> > >> Hi
        Vitaly, >
            >> I did it because I read from > >> > >
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
            > >> that says: > >> "One solution is to simply > comment
        out > (or
           delete) > the lines > of code out > >> in the file where it is >
           included > for the > second time > i.e., > ..". So if it is >
         >> the
           case I am going to > undo it > to see what > happens... > I
        will >
           let you know. > >> Thanks/Jamie > >> On Mon, Aug 10, 2009 at
         > 5:05
           PM, > Vitaly > V. Chaban > > > > >> > > > > >>> > > > > > >>
         > > > >
            >>>> > > > > >> > > > > >>> > > > > > >> > > > > >>>>>> > > > >>
           wrote: > >>> > >>> Why did you comment out > [defaults] in >
           ffoplsaa.itp? The > general idea > >>> is that the sections
        in the >
           resulting > topology file > (after > including > >>> #include's)
           must be > placed in the > strict order. > > > > > >
------------------------------------------------------------------------
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-- ========================================

    Justin A. Lemkul
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    ICTAS Doctoral Scholar
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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