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
