<div>Hi Justin,</div>
<div>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 the same number. I still get the same Note. Should I assigned the same 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??</div>
<div>Thanks a lot/Jamie<br><br></div>
<div class="gmail_quote">On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Justin,
<div class="im"><br>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<br>
<br></div></blockquote><br>Please see the manual, section 4.6.2. I don't know what you mean by separating your structure.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div></div>
<div class="h5">On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br> Jamie Seyed wrote: > Dear Justin, > Thanks for your all valuable<br> comments. Actually I got these 2 notes: ><br> -----------------------------------------------------------------------------------<br>
> > NOTE 1 [file topol.top, line unknown]: > The largest charge<br> group contains 24 atoms. > Since atoms only see each other when the<br> centers of geometry of the charge > groups they belong to are within<br>
the cut-off distance, too large charge > groups can lead to serious<br> cut-off artifacts. > For efficiency and accuracy, charge group<br> should consist of a few atoms. > For all-atom force fields use: CH3,<br>
CH2, CH, NH2, NH, OH, CO2, CO, etc. > > NOTE 2 [file md.mdp, line<br> unknown]: > You are using a plain Coulomb cut-off, which might<br> produce artifacts. > You might want to consider using PME<br> electrostatics. > ><br>
------------------------------------------------- > > How I can<br> trust my results specially for first one?? Many Thanks/Jamie > You<br> should define smaller charge groups. The tip given in the note is<br>
useful. As for note 2, never use cut-off for electrostatics. It is<br> not as reliable as PME. -Justin > > > On Mon, Aug 10, 2009 at 9:18<br> PM, Justin A. Lemkul > wrote: > > > > Jamie Seyed wrote: > > The gro<br>
file: > ------------------------- > GROtesk MACabre and Sinister ><br> 1836 > 12 C 1 1.311 1.563 0.994 > 12 C 2 1.220 1.635 1.079 > 12 C 3<br> 1.092 1.565 1.081 > 12 C 4 1.108 1.449 0.996 > ......... > > 12 H<br>
118 1.438 1.092 1.244 > 12 H 119 1.413 1.098 1.426 > 12 H 120 1.291<br> 1.033 1.329 > 2SOL OW 121 0.569 1.275 1.165 > 2SOL HW1 122 0.476<br> 1.268 1.128 > 2SOL HW2 123 0.580 1.364 1.209 > > ....... > > 572SOL<br>
HW2 1833 2.024 1.991 2.158 > 573SOL OW 1834 2.290 2.286 2.382 ><br> 573SOL HW1 1835 2.320 2.214 2.320 > 573SOL HW2 1836 2.251 2.246<br> 2.465 > 2.64467 2.64467 2.64467 > ><br> ----------------------------------------- > and itp-file: > ><br>
----------------- > > ; Include forcefield parameters > > [<br> moleculetype ] > ; Name nrexcl > C60CH3 3 > > [ atoms ] > ; nr type<br> resnr residue atom cgnr charge > mass typeB chargeB massB > 1<br>
opls_145 1 C60CH3 C 1 0 > 12.011 ; qtot 0 > 2 opls_516 1 C60CH3 C 2<br> 0 > 12.011 ; qtot 0 > ..... > > > 71 78 79 69 3 1.740000e+02<br> 5.000000e+00 > 3.000000e+00 1.740000e+02 5.000000e+00 3.000000e+00 ><br>
69 79 80 2 3 2.580000e+02 5.000000e+00 > 3.000000e+00 2.580000e+02<br> 5.000000e+00 3.000000e+00 > > [ system ] > ; Name > C60CH3 > > [<br> molecules ] > ; Compound #mols > C60CH3 1 ><br>
----------------------------------------------- > > Oh Ok now I<br> understand that I should remove only one of the > [molecule] > > ><br> The [ system ] and [ molecules ] directives *only* belong in the ><br>
system .top, never in an .itp file. Remove both [ system ] and [ ><br> molecules ] from the .itp, and list the appropriate molecules in the<br> > [ molecules ] directive of the .top only. > > -Justin > ><br>
sections in itp-file (right)?? > > Thanks a lot/ Please let me know<br> if still something is > missing.../Thanks/Jamie > > > On Mon, Aug<br> 10, 2009 at 8:42 PM, Justin A. Lemkul > > >> wrote: > > > > Jamie<br>
Seyed wrote: > > First I put 1000, but after editconf and genbox it<br> has been > changed to 572. I only have 1 part with SOL 572... > > ><br> I'm thoroughly confused. There is no need to manually manipulate ><br>
these sections if you're allowing genbox, genion, etc to ><br> manipulate > them for you. Please post the following information to<br> get a > resolution: > > 1. Your .top file > 2. Your molecule.itp<br>
file (you can delete out lines in the atoms, > bonds, dihedrals<br> section so the file is not unnecessarily > long - I'm > really just<br> interested in the other directives that may be > present) > ><br>
-Justin > > On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul > > ><br> > > >>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, > > Thanks<br> again... . Actully I have a question: I > have 1836 > atoms > (572<br>
water and 1 molecule with 120 atoms). In top > of my > file.gro > I<br> have 1836 and in topology in [molecules] I have > c60ch3 > 1; and ><br> SOL 572 which means the same as above. So how I should > change it ><br>
to get rid of error...??/ > > > The above should be correct.<br> However, you then have > in your .top > you posted earlier: > > ><br> [molecules] > molecule 1 > SOL 1000 > > This section is probably the<br>
source of your problem. > Again, as I > said before, there should<br> only ever be one [ molecules ] > section in > the .top file. Sounds<br> like you've got two. > > -Justin > > Thank you in advance.../Jamie ><br>
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul > > > > > >> > > ><br> > > >>>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, > Oh yes.<br> I had a line that include ff again > and I > deleted that > (is that<br>
ok)? now I got a new error related to > "number of > coordinates in<br> > > > That's more than OK, that's correct. As Mark > pointed > out,<br> there > should only ever be one invocation of [ > defaults ] in > a<br>
topology. > > > coordinate file does not match topology..." I ><br> should fix this > one now!! Simple one to > fix. Figure out where<br> the duplicate or > missing > molecules are within the topology. I'm<br>
> guessing your > molecule.itp > was really a molecule.top,<br> complete with [ > defaults ], [ > system ], > and [ molecules ]<br> directive, right? None of these > should be > present > in an .itp<br>
file, only a .top. > > -Justin > > Thanks a lot/Jamie > > > On Mon,<br> Aug 10, 2009 at 8:10 PM, Justin A. > Lemkul > > > > > >> > > > > ><br> >>> > > > > >> > > > > > >>>>> wrote: > > > Can you post the<br>
contents of > molecule.itp? The > first > #include for > the force<br> field is likely not the problem; > you've probably > #included > it<br> again in molecule.itp. > > -Justin > > Jamie Seyed wrote: > > Dear<br>
all, > I have a topology contains line as > below. I > do not ><br> understand > what is wrong with it that I get an > error ><br> ----------- > Program grompp, Version 4.0.5 > Source Code file:<br>
topio.c, line: 415 > Fatal error: > Syntax error-File ffoplsaa.itp,<br> line 18 > last line read: > '[defaults]' > Invalid order for<br> directive defaults > -------------- > according to the page > ><br>
<a href="http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file</a><br> > I do not have twice default > section... SO I > do not > know ><br>
exactly > which files I should check... It says > topology and ff. ><br> Topology > that I am using in grompp is as > below and the ><br> ffoplsaa.itp has > only one default section... > Would you please<br>
help me to solve > the problem. > topol.top: ------------- ><br> #include "ffoplsaa.itp" > #include "spce.itp" > #include<br> "molecule.itp" > [system] > fullerene in water > [molecules] ><br>
molecule 1 > SOL 1000 > -------------------- > Many Thanks in<br> Advance and I > appreciate your > help/Jamie > > On Mon, Aug 10,<br> 2009 at 5:46 PM, > Jamie Seyed > > > > > >> > > > > >>> > > > > > >><br>
> > > > >>>> > > > > >> > > > > > >>> > > > >> > > > > > >>>>>> > ><br> wrote: > > Dear Vitaly, > topol.top: ------------- > #include<br>
"ffoplsaa.itp" > #include "spce.itp" > #include "c80ch3.itp" ><br> [system] > fullerene in water > [molecules] > C80CH3 1 > SOL 1000 ><br> -------------------- > my command is: > grompp -f md.mdp -c f.gro -p<br>
> topol.top > -o pr.tpr > -maxwarn 10 > Thank you for helping me<br> out to > solve the > problem/ > Regards/Jamie > On Mon, Aug 10, 2009<br> at > 5:39 PM, > Vitaly > V. Chaban > > > > > >> > > > > >>> > > > ><br>
> >> > > > > >>>> > > > > >> > > > > >>> > > > > > >> > > > ><br> >>>>>> wrote: > > Jamie, > > The idea is the same. Some > directive<br>
> is not > at its > place. I > cannot say > which is exactly<br> because I > don't see > all the > picture with > your > topology<br> file (+included files). > Write the > sequence of > directives as ><br>
they go in .top (+included > .itp) and > then > we will see > what<br> sections > must be shifted or maybe just > swapped. > > Vitaly > ><br> On Tue, Aug 11, 2009 at 12:34 > AM, Jamie > Seyed > > > >> > > > ><br>
>>> > > > > >> > > > > > >>>> > > > > > >> > > > > > >>> > > > > ><br> >> > > > > > >>>>>> wrote: > > Hi Vitaly, > > When I add it back, I<br>
got > the old > error > > ----------- > > Program grompp, Version<br> 4.0.5 > > Source Code file: topio.c, > line: 415 > > Fatal error: ><br> > Syntax error-File > ffoplsaa.itp, > line 18 > > last line read: ><br>
> '[defaults]' > > Invalid order for > directive defaults > ><br> ----------- > > Now do you have any idea??? I > appreciate > your ><br> help/Jamie > > > > On Mon, Aug 10, 2009 at > 5:22 PM, > Jamie Seyed<br>
> > > > >> > > > > > >>> > > > >> > > > > > >>>> > > > > >> > > > ><br> > >>> > > > >> > > > > > >>>>>> > > wrote: > >> > >> Hi Vitaly, ><br>
>> I did it because I read from > >> > ><br> <a href="http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file</a><br>
> >> that says: > >> "One solution is to simply > comment out > (or<br> delete) > the lines > of code out > >> in the file where it is ><br> included > for the > second time > i.e., > ..". So if it is > >> the<br>
case I am going to > undo it > to see what > happens... > I will ><br> let you know. > >> Thanks/Jamie > >> On Mon, Aug 10, 2009 at > 5:05<br> PM, > Vitaly > V. Chaban > > > > >> > > > > >>> > > > > > >> > > > ><br>
>>>> > > > > >> > > > > >>> > > > > > >> > > > > >>>>>> > > > >><br> wrote: > >>> > >>> Why did you comment out > [defaults] in ><br>
ffoplsaa.itp? The > general idea > >>> is that the sections in the ><br> resulting > topology file > (after > including > >>> #include's)<br> must be > placed in the > strict order. > > > > > ><br>
------------------------------------------------------------------------<br> > > > > > _______________________________________________ ><br> gmx-users mailing list > <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>> > > > >> > > > > >>> > > > > >> > > >
<div class="im"><br> > > >>>> > > > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> > Please search the archive at > <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> ><br>
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> ======================================== > > Justin A. Lemkul ><br> Ph.D. Candidate > ICTAS Doctoral Scholar > Department of<br> Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a><br>
</div> <<a href="http://vt.edu/" target="_blank">http://vt.edu</a>> > > > | (540) > > 231-9080 > > >
<div class="im"><br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a> > ><br> ======================================== > ><br>
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======================================== > > Justin A. Lemkul ><br> Ph.D. Candidate > ICTAS Doctoral Scholar > Department of<br> Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a><br>
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======================================== > > Justin A. Lemkul ><br> Ph.D. Candidate > ICTAS Doctoral Scholar > Department of<br> Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a><br>
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Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia<br></div> Tech Blacksburg, VA jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu</a>> | (540)
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>
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