[gmx-users] Re: Carbon Nanotube Simulation Issues
Yang Ye
leafyoung at yahoo.com
Fri Jul 27 19:31:02 CEST 2007
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
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> posting!
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
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