[gmx-users] Re: Carbon Nanotube Simulation Issues
Yang Ye
leafyoung at yahoo.com
Thu Jul 26 19:25:24 CEST 2007
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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