VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 05 2010 - 11:56:07 CDT

On Mon, Apr 5, 2010 at 12:33 PM, Ranyere Deyler <ranyere_at_gmail.com> wrote:

> And nothing. Looking at the console it gave this message:
>
> WARNING: PSF file is incomplete, no angles, dihedrals, impropers, or
> cross-terms will be writen.
>
> So, it didn't wright down anything, not even the bonds. I tried everything
> but it always generate a wrong psf file. If you have another idea i
> apreciate. Thanks a lot.
>

the message is not important. this message is only printed
when you don't write out angles and dihedrals. it doesn't say
anything about the bonds. have a look at the psf file itself!

you can in principle silence the message by using:
topo guessangles
to generate the corresponding angle definitions, similarly
for dihedrals and impropers, but you have to check the literature
on which definitions would be a good idea to include
or whether it would be sufficient to just do a position
restraint on the CNT atoms.

in general, if you want a realistic description of a CNT
you should use an AIREBO or Tersoff many body
potential and those don't need any of the two.

cheers,
    axel.

> Ranyere Deyler Trindade
>
> On Mon, Apr 5, 2010 at 11:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, 2010-04-05 at 10:58 -0300, Ranyere Deyler wrote:
>> > Dear VMD Users,
>> >
>> > I generated a carbon nanotube by the plugin in VMD. Well, it
>> > recognizes the bonds on the nanotubes but when i give the
>> >
>> > set sel [atomselect all]
>> > $sel writepdb file.pdb
>> > $sel writepsf file.psf
>> >
>> > it doesn't add any bonds on the psf file. It shows the bonds on the
>> > console when you create the nanotube but when you write down the psf
>> > file it doesn't.
>>
>> can you please try if issuing the "topo retypebonds" command
>> after building the carbon nanotube solves the bond writing issue.
>>
>> > So i'm wondering if there's a better way of generating the psf of the
>> > CNT.
>> >
>> > I tryed using the AutomaticPsf Builder but it was not successful, it
>> > gives some erros, it says that 'CNT' is not parametrised. And if
>>
>> psfgen (which autopsf is a front end for) cannot work for these
>> kinds of systems.
>>
>> cheers,
>>    axel.
>>
>> > someonet has the proper topology file for a carbon nanotubes (as the
>> > ones in the tutorial water trough nanotubes, that already gives the
>> > psf but it doesn't have the topology file that generated it), i would
>> > apreciate.
>> > Thanks a lot
>> >
>> > Ranyere Deyler Trindade
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
>> http://sites.google.com/site/akohlmey/
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.