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 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
