[gmx-users] Re: Carbon Nanotube Simulation Issues

Yang Ye leafyoung at yahoo.com
Wed Jul 25 17:05:28 CEST 2007


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.

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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