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
On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul <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 > > > >> > > > > >>> > > > > >> > > > > > > >>>> > > > 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 > > > -- > > ======================================== > > 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 > > > > -- > ======================================== > > 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 > > > > > -- ======================================== > > 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 > > > > -- > ======================================== > > 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 > > > > -- > > ======================================== > > 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 > > -- > ======================================== 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-usersPlease 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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