They are in the ffgmx.itp file and maybe I missed it but I didn't read about people having to change it for CNT's, but maybe so I will look further into this and try some things... I will let you guys know where I get. Also if any one knows already knows please feel free to give me a hint or ref.
Thanks so much, ~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 Robert Johnson >Sent: Friday, July 27, 2007 10:28 AM >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues > >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:gmx-users- >[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 _______________________________________________ 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
