[gmx-users] Re: Carbon Nanotube Simulation Issues
Christopher Stiles
CS145331 at albany.edu
Fri Jul 27 16:17:58 CEST 2007
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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>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ------------------------------
>>>>>>
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