[gmx-users] Re: Carbon Nanotube Simulation Issues

Robert Johnson bobjohnson1981 at gmail.com
Fri Jul 27 16:27:48 CEST 2007


Did you define angle and dihedral parameters in the [ angletypes ] and
[ dihedraltypes ] sections of your .itp file?
Bob

On 7/27/07, Christopher Stiles <CS145331 at albany.edu> 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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> >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: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >>>>>
> >>> bounces at gromacs.org]
> >>>
> >>>>> 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 at 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 gmx-users-request at gromacs.org.
> >>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>> ------------------------------
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> gmx-users mailing list
> >>>>>> gmx-users at 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 at 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 gmx-users-request at gromacs.org.
> >>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> _______________________________________________
> >>>>> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>>
> >>>>>
> >>>> _______________________________________________
> >>>> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>
> >>>>
> >>>>
> >>> _______________________________________________
> >>> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >
> >_______________________________________________
> >gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



More information about the gromacs.org_gmx-users mailing list