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 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?? Thanks a lot/Jamie
On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <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>> 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. > > > > > > >> >> ------------------------------------------------------------------------ >> > > > > > _______________________________________________ > >> gmx-users mailing list > gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> > > > >> > > > > >>> > > > > >> > > > >> > > >>>> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at > http://www.gromacs.org/search > >> before posting! > Please don't post (un)subscribe > requests to the >> > list. Use the > www interface or send it to > >> gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org> >> > > > > > >> > > > > > >>> > > > > > > >> > > > > > >>>>. > > Can't >> post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- >> > ======================================== > > Justin A. Lemkul > >> Ph.D. Candidate > 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 > > >> ======================================== > > >> _______________________________________________ > gmx-users mailing >> list > gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > > >> >> > > > > >>> > > > > > >> > > > > >>>> > > > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search >> the archive at > http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests > to the > list. > Use the >> www > interface or send it to > gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> > > > > > >> > > > > > >>> > >> > > > > >> > > > > > >>>>. > > Can't post? Read > >> http://www.gromacs.org/mailing_lists/users.php > > > > -- >> ======================================== > > Justin A. Lemkul > >> Ph.D. Candidate > 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 > > >> ======================================== > >> _______________________________________________ > gmx-users mailing >> list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > > > >> >> > > > > >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > http://www.gromacs.org/search before >> > posting! > Please don't post (un)subscribe requests to the > >> list. > Use the www > interface or send it to > >> gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org> >> > > > > >> > > > > > >>>. > Can't post? Read > >> http://www.gromacs.org/mailing_lists/users.php > > > > -- >> ======================================== > > Justin A. Lemkul > >> Ph.D. Candidate > 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 > > >> ======================================== > >> _______________________________________________ > gmx-users mailing >> list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > > > >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please >> search the archive at > http://www.gromacs.org/search before > >> posting! > Please don't post (un)subscribe requests to the list. > >> Use the www > interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> > > > > > >>. > Can't post? >> Read > http://www.gromacs.org/mailing_lists/users.php > > > > -- >> ======================================== > > Justin A. Lemkul > >> Ph.D. Candidate > 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 > > >> ======================================== > >> _______________________________________________ > gmx-users mailing >> list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search >> the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> > > >. > Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php > > > > -- > >> ======================================== > > Justin A. Lemkul > >> Ph.D. Candidate > 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 > > >> ======================================== > >> _______________________________________________ > gmx-users mailing >> list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search >> the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> > . > Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php > > -- >> ======================================== Justin A. Lemkul Ph.D. >> Candidate 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 >> ======================================== >> _______________________________________________ gmx-users mailing >> list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search >> the archive at http://www.gromacs.org/search before posting! Please >> don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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