Just do a quick literature serach for MD simulations of carbon nanotubes and see what other people are using. For example, Nature, Vol 351, p. 464 and others.
One error that I see is that th0 should be 120 (sp2 carbons form planar hexagonal rings). A th0 of 109.5 is really going to distort your nanotube. Bob On 7/30/07, Christopher Stiles <[EMAIL PROTECTED]> wrote: > So I get grompp to run with zero errors now, I have done this by defining > the following 2 lines in my ffgmxbon.itp file: > #################################### > [ angletypes ] > ; i j k func th0 cth > C C C 1 109.500 397.480 > #################################### > [ dihedraltypes ] > ; i l func q0 cq > C C 1 0.000 167.360 > #################################### > ***The last line of each was the addition > > My question is are these proper/acceptable values for a (6,6) SWCNT (single > wall carbon nanotube)? > Thanks so much, > > ~Christopher Stiles > College of Nanoscale Science and Engineering (CNSE) > State University of New York, Albany, New York 12203, USA > _________________________________________________________ > > >You could probably dispense with the dihedral terms (as long as you > >aren't interested in the mechanical properties of the CNT), but I > >would at least include a bond and angle term for the nanotube atoms. > > > > > >On 7/27/07, Yang Ye <[EMAIL PROTECTED]> wrote: > >> On one hand, use -pp for grompp for whatever warnings, so you may what's > >> on the line which causes problems. > >> On the other hand, find force field parameters for carbon nanotubes. For > >> a simple rigid nanotube, I reckon that you may only need bond potential > >> for every bond. > >> > >> On 7/27/2007 10:42 PM, Christopher Stiles wrote: > >> > 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:gmx-users- > >[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 > >> > > >> > > >> > >> _______________________________________________ > >> 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