[gmx-users] Re: Carbon Nanotube Simulation Issues
Christopher Stiles
CS145331 at albany.edu
Fri Jul 27 16:42:04 CEST 2007
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
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>> >>>>>>>
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>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
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