Did you define angle and dihedral parameters in the [ angletypes ] and [ dihedraltypes ] sections of your .itp file? Bob
On 7/27/07, Christopher Stiles <[EMAIL PROTECTED]> wrote: > The warnings are: > ... > WARNING 701 [file "SWNT_6_6_144.top", line 1278]: > No default Angle types, using zeroes > WARNING 702 [file "SWNT_6_6_144.top", line 1278]: > No default Angle types for perturbed atoms, using normal values > ... > WARNING 793 [file "SWNT_6_6_144.top", line 1327]: > No default Proper Dih. types, using zeroes > WARNING 794 [file "SWNT_6_6_144.top", line 1327]: > No default Proper Dih. types for perturbed atoms, using normal values > ... > Those are the 2 errors, here is a link to the full output: > http://cs86.com/CNSE/files/Grompp_Output.txt > > Thank you again, > > ~Christopher Stiles > College of Nanoscale Science and Engineering (CNSE) > State University of New York, Albany, New York 12203, USA > > > >-----Original Message----- > >From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > >On Behalf Of Yang Ye > >Sent: Friday, July 27, 2007 4:45 AM > >To: Discussion list for GROMACS users > >Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues > > > >On 7/27/2007 4:53 AM, Christopher Stiles wrote: > >> Ok here is the update: > >> I have made the following changes: > >> I almost doubled my box size and limited the saturation to 256 water > >> molecules. > >> I removed the include from my *.mdp file > >> Changed the includes in my topology file to: > >> #include "ffgmx.itp" > >> #include "spc.itp" > >> And added the following line of code to the [ bondtype ] section of the > >> ffgmxbon.itp file: > >> C C 1 0.14210 478900. > >> > >> I use the files in this zip file to run grompp: > >> > >> http://cs86.com/CNSE/SWNT.zip > >> > >> running grompp I use the following command: > >> grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top > >> -maxwarn 10000 -pp > >> > >What's the warnings? > >> It works but there is 1176 warnings, which I am assuming this is a > >problem? > >> Then I run mdrun using the following command: > >> Mdrun -s topol.tpr > >> It works just fine > >> Then I can view it with ngmx using the following command: > >> ngmx -f traj.xtc -s topol.tpr. > >> This works just fine as well. > >> > >> My question is are the warnings ok/normal or is there some fix that needs > >to > >> be made? > >> > >> Thank you again Yang, Bob, and every one else you have all been a great > >> help! > >> > >> ~Christopher Stiles > >> College of Nanoscale Science and Engineering (CNSE) > >> State University of New York, Albany, New York 12203, USA > >> > >> ________________________________________________ > >> > >> > >>> You shall include ffgmx.itp only and make change to ffgmxbon.itp. > >>> > >>> On 7/27/2007 12:18 AM, Christopher Stiles wrote: > >>> > >>>> Yang & Bob, > >>>> > >>>> When I change the include to be ffgmxbon.itp instead of ffgmx.itp I get > >>>> > >>> the > >>> > >>>> following error: > >>>> **************************** > >>>> Fatal error: > >>>> Invalid order for directive bondtypes, file ""ffgmxbon.itp"", line 1 > >>>> **************************** > >>>> I believe it is because when just including ffgmxbon.itp it never calls > >>>> > >>> up > >>> > >>>> ffgmxnb.itp so there for atomtypes are not defined first ect... > >>>> Although my understanding of this whole process is very limited... > >>>> > >>>> Thank you all very much for your patience and guidance helping me > >along! > >>>> > >>>> ~Christopher Stiles > >>>> College of Nanoscale Science and Engineering (CNSE) > >>>> State University of New York, Albany, New York 12203, USA > >>>> > >>>> ________________________________________________ > >>>> > >>>> > >>>> > >>>>> -----Original Message----- > >>>>> From: [EMAIL PROTECTED] [mailto:gmx-users- > >>>>> > >>> [EMAIL PROTECTED] > >>> > >>>>> On Behalf Of Yang Ye > >>>>> Sent: Thursday, July 26, 2007 11:34 AM > >>>>> To: Discussion list for GROMACS users > >>>>> Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues > >>>>> > >>>>> Hi, > >>>>> > >>>>> It's my typo again. Sorry. It shall be ffgmxbon.itp. > >>>>> > >>>>> On 7/26/2007 10:57 PM, Christopher Stiles wrote: > >>>>> > >>>>> > >>>>>> Yang, > >>>>>> Thank you again for being so detailed. I do have 2 questions > >though, > >>>>>> when you say: > >>>>>> > >>>>>> > >>>>>> > >>>>>>> So you shall change ffG43b1.itp to ffgmx.itp. And add the line > >>>>>>> C C 1 0.14210 478900. > >>>>>>> > >>>>>>> To the end of section [ bondtypes ], not the end of the whole file. > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> You mean in the topology file I assume for the changing from > >>>>>> > >>> ffG43b1.itp > >>> > >>>>> to > >>>>> > >>>>> > >>>>>> ffgmx.itp. But the adding of the line is what I am having trouble > >with, > >>>>>> should it go in the topology file or ffgmx.itp? because neither have > >a > >>>>>> [ bondtypes ] section and when I add one it just gives me errors. > >From > >>>>>> > >>>>>> > >>>>> what > >>>>> > >>>>> > >>>>>> I understand from the manual it is only the *.itp files that can have > >>>>>> > >>>>>> > >>>>> those > >>>>> > >>>>> > >>>>>> sections, so I think maybe it should go in the ffgmx.itp file I am > >just > >>>>>> > >>>>>> > >>>>> not > >>>>> > >>>>> > >>>>>> making the addition to the file properly. > >>>>>> Also here is a copy of the ffgmx.itp file: > >>>>>> ######################## > >>>>>> #define _FF_GROMACS > >>>>>> #define _FF_GROMACS1 > >>>>>> > >>>>>> [ defaults ] > >>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > >>>>>> 1 1 no 1.0 1.0 > >>>>>> > >>>>>> #include "ffgmxnb.itp" > >>>>>> #include "ffgmxbon.itp" > >>>>>> ######################## > >>>>>> And here is a copy of my ffG43b1.itp file: > >>>>>> ######################## > >>>>>> #define _FF_GROMOS96 > >>>>>> #define _FF_GROMOS43B1 > >>>>>> > >>>>>> [ defaults ] > >>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > >>>>>> 1 1 no 1.0 1.0 > >>>>>> > >>>>>> #include "ffG43b1nb.itp" > >>>>>> #include "ffG43b1bon.itp" > >>>>>> ######################## > >>>>>> > >>>>>> Last of all this question is to any one, how do I reply to a specific > >>>>>> thread? I have searched around and I have had no luck. > >>>>>> > >>>>>> Thank you so much for all of your help! > >>>>>> > >>>>>> ~Christopher Stiles > >>>>>> College of Nanoscale Science and Engineering (CNSE) > >>>>>> State University of New York, Albany, New York 12203, USA > >>>>>> > >>>>>> _______________________________________________________ > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I missed one dash in the front. So it should be > >>>>>> > >>>>>> include = -IffG43b1.n2t > >>>>>> > >>>>>> The problem you had was because of improper usage of include, for > >every > >>>>>> > >>>>>> > >>>>> item > >>>>> > >>>>> > >>>>>> to be put in include=, you shall prefix -I in the front. Since you > >have > >>>>>> > >>>>>> > >>>>> not > >>>>> > >>>>> > >>>>>> put it, cpp couldn't finish parsing the topology file, so your > >topology > >>>>>> contains nothing. > >>>>>> > >>>>>> ffG43b1.n2t is not necessary for grompp. > >>>>>> > >>>>>> You shall include spc.itp in your topology file to include the > >topology > >>>>>> > >>>>>> > >>>>> for > >>>>> > >>>>> > >>>>>> water. So your file header shall be like > >>>>>> > >>>>>> #include "ffG43b1.itp" > >>>>>> #include "spc.itp" > >>>>>> > >>>>>> Last and most important, the line you added to ffgmxbon.itp is > >useless > >>>>>> because you are using GROMOS96 force field. > >>>>>> > >>>>>> So you shall change ffG43b1.itp to ffgmx.itp. And add the line > >>>>>> C C 1 0.14210 478900. > >>>>>> > >>>>>> To the end of section [ bondtypes ], not the end of the whole file. > >>>>>> > >>>>>> So the command line without -maxwarn can work properly. Note that you > >>>>>> > >>>>>> > >>>>> shall > >>>>> > >>>>> > >>>>>> not use -maxwarn in most cases. > >>>>>> grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p > >>>>>> SWNT_6_6_144_post_genbox.top -pp > >>>>>> > >>>>>> The suffix _s is just what I have specified for my build. You don't > >>>>>> > >>> need > >>> > >>>>> the > >>>>> > >>>>> > >>>>>> same setting. > >>>>>> > >>>>>> Regards, > >>>>>> Yang Ye > >>>>>> > >>>>>> > >>>>>> On 7/25/2007 10:29 PM, Christopher Stiles wrote: > >>>>>> > >>>>>> > >>>>>> > >>>>>>> Yang, > >>>>>>> Thank you very much for you help. I am sorry I did not think to > >>>>>>> > >>> package > >>> > >>>>> my > >>>>> > >>>>> > >>>>>>> files and commands up I will do so by the end of the day. As to the > >>>>>>> ffG43b1.n2t it was to get x2top to work, it defines single and > >double > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> bonded > >>>>>> > >>>>>> > >>>>>> > >>>>>>> carbon so that I do not have to cap my tube with hydrogen. Although > >I > >>>>>>> > >>> am > >>> > >>>>>>> > >>>>>> not > >>>>>> > >>>>>> > >>>>>> > >>>>>>> sure how you got the include to work with: > >>>>>>> include = IffG43b1.n2t > >>>>>>> Do you have a file named IffG43b1.n2t in your lib or your working > >dir? > >>>>>>> The file comes from the ffgmx.n2t file in the Gromacs lib but the > >name > >>>>>>> > >>>>>>> > >>>>> is > >>>>> > >>>>> > >>>>>>> changes to ffG43b1.n2t and the following 2 lines are added: > >>>>>>> C C 1 C ; CNT Carbon with > >>>>>>> > >>> one > >>> > >>>>>>> > >>>>>> bond > >>>>>> > >>>>>> > >>>>>> > >>>>>>> C C 2 C C ; CNT double bonded > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> Carbon > >>>>>> > >>>>>> > >>>>>> > >>>>>>> Next must I use grompp_s? (I believe this is grompp with single > >>>>>>> > >>>>>>> > >>>>> accuracy, > >>>>> > >>>>> > >>>>>>> correct?) Because if so I will have to compile it. > >>>>>>> Last question, by it gives a pass do you mean you get a little over > >>>>>>> > >>> 1500 > >>> > >>>>>>> warnings and then get the following: > >>>>>>> Fatal error: > >>>>>>> No such moleculetype SOL > >>>>>>> > >>>>>>> Thank you so much for your help I really appreciate it, > >>>>>>> > >>>>>>> ~Christopher Stiles > >>>>>>> College of Nanoscale Science and Engineering (CNSE) > >>>>>>> State University of New York, Albany, New York 12203, USA > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> Sorry that most of us on the list were too busy to read one full > >page > >>>>>>>> > >>>>>>>> > >>>>> of > >>>>> > >>>>> > >>>>>>>> details and download individual files. We might just prefer to > >>>>>>>> > >>> download > >>> > >>>>>>>> one package, and run a script file for us quickly dive into the > >>>>>>>> > >>>>>>>> > >>>>> problem. > >>>>> > >>>>> > >>>>>>>> Is include in mdout_test.mdp a standard option? Where did you get > >it? > >>>>>>>> > >>> I > >>> > >>>>>>>> changed it to > >>>>>>>> > >>>>>>>> include = IffG43b1.n2t > >>>>>>>> > >>>>>>>> It works. Otherwise, cpp terminates before it generates a full top. > >>>>>>>> grompp -pp is always a good friend for grompp error (and thorough > >>>>>>>> reading of chapter 5 of manual). > >>>>>>>> > >>>>>>>> Next issue comes the format of ffG43b1.n2t. I don't think it > >conforms > >>>>>>>> > >>>>>>>> > >>>>> to > >>>>> > >>>>> > >>>>>>>> any GROMACS topology format. Again where does it comes from? > >>>>>>>> > >>>>>>>> My grompp command line: > >>>>>>>> grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p > >>>>>>>> SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp > >>>>>>>> > >>>>>>>> It gives a pass, at least. > >>>>>>>> > >>>>>>>> Hope you can work further on. > >>>>>>>> > >>>>>>>> Regards, > >>>>>>>> Yang Ye > >>>>>>>> > >>>>>>>> On 7/25/2007 2:41 AM, Christopher Stiles wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>> I am trying to simulate a single wall carbon nanotube in a box > >>>>>>>>> solvated in water, at 300k for about 200ps. Also once I accomplish > >>>>>>>>> this I wish to fix either one end of the tube or fix the center of > >>>>>>>>> mass position, although this part is unimportant if I can not get > >>>>>>>>> > >>> the > >>> > >>>>>>>>> thing to run at all yet. > >>>>>>>>> > >>>>>>>>> I have created a page with a full detailed account of what I have > >>>>>>>>> > >>> done > >>> > >>>>>>>>> and tried so far. http://cs86.com/CNSE/SWNT.htm > >>>>>>>>> > >>>>>>>>> Please note all files where created with Vim in the unix > >environment > >>>>>>>>> so I think I have eliminated the formatting issues. > >>>>>>>>> > >>>>>>>>> Also that I have tried the simulation with many different sized > >>>>>>>>> > >>> tubes > >>> > >>>>>>>>> from TubeGen > >(http://turin.nss.udel.edu/research/tubegenonline.html > >>>>>>>>> > >>> ), > >>> > >>>>>>>>> both with and without hydrogen capped ends (this is something I > >have > >>>>>>>>> read in the archives as a possible solution, it makes no > >difference > >>>>>>>>> > >>> in > >>> > >>>>>>>>> the end). > >>>>>>>>> > >>>>>>>>> I have come to the conclusion through the help of many of you that > >>>>>>>>> > >>> the > >>> > >>>>>>>>> *.pdb file from TubeGen and mainly the residue UNK among other > >>>>>>>>> things. If any one has had luck with using a TubeGen file to > >create > >>>>>>>>> > >>> a > >>> > >>>>>>>>> simulation please let me know as to how. Other wise I am looking > >at > >>>>>>>>> > >>> a > >>> > >>>>>>>>> few new options basically all of them involve writing my own > >files. > >>>>>>>>> > >>>>>>>>> I guess I am looking for advice where to go from here. > >>>>>>>>> > >>>>>>>>> ~Christopher Stiles > >>>>>>>>> College of Nanoscale Science and Engineering (CNSE) > >>>>>>>>> State University of New York, Albany, New York 12203, USA > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>>>> http://www.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 [EMAIL PROTECTED] > >>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> ------------------------------ > >>>>>> > >>>>>> _______________________________________________ > >>>>>> gmx-users mailing list > >>>>>> gmx-users@gromacs.org > >>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>>> Please search the archive at http://www.gromacs.org/search before > >>>>>> > >>>>>> > >>>>> posting! > >>>>> > >>>>> > >>>>>> _______________________________________________ > >>>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>>> http://www.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 [EMAIL PROTECTED] > >>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>> _______________________________________________ > >>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>> http://www.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 [EMAIL PROTECTED] > >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>>> > >>>>> > >>>> _______________________________________________ > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://www.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 [EMAIL PROTECTED] > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>> > >>>> > >>>> > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://www.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 [EMAIL PROTECTED] > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >> > >> > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> > > > >_______________________________________________ > >gmx-users mailing list gmx-users@gromacs.org > >http://www.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 [EMAIL PROTECTED] > >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
