[gmx-users] Re: Carbon Nanotube Simulation Issues
Christopher Stiles
CS145331 at albany.edu
Mon Jul 30 17:23:08 CEST 2007
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
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
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>> >>>>>>>>
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>> >>>>>>>>
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>http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>> ------------------------------
>> >>>>>>>>>
>> >>>>>>>>> _______________________________________________
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>> >>>>>>>>
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>> >>>>>>>>>
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>> >>>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> 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
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>> >>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>> >>>> 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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