[gmx-users] Re: Carbon Nanotube Simulation Issues
Christopher Stiles
CS145331 at albany.edu
Thu Jul 26 22:53:57 CEST 2007
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
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
>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------
>>>>
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