[gmx-users] Re: Carbon Nanotube Simulation Issues
Yang Ye
leafyoung at yahoo.com
Fri Jul 27 10:44:47 CEST 2007
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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> ------------------------------
>>>>>
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