[gmx-users] Re: Carbon Nanotube Simulation Issues

Robert Johnson bobjohnson1981 at gmail.com
Mon Jul 30 18:14:22 CEST 2007


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 <CS145331 at albany.edu> 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 <leafyoung at yahoo.com> 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: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >bounces at gromacs.org]
> >> >> 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 <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
> >> >>>
> >> >>>
> >> >> _______________________________________________
> >> >> 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
>



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