[gmx-users] Re: Carbon Nanotube Simulation Issues

Robert Johnson bobjohnson1981 at gmail.com
Thu Jul 26 17:11:02 CEST 2007 

Hi Chris,
Yes, the bondtypes, etc. sections go in the .itp file.

The only way (I know of) to respond to a specific thread is to have an
email from that thread.
Bob

On 7/26/07, Christopher Stiles <CS145331 at albany.edu> 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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