VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 18 2019 - 13:14:00 CST

you didn't report tbe topotools version
the data file itself is useless without the original file that you used.

you know that you can build a proper graphene structure directly from
within VMD, right?

axel.

‪On Mon, Feb 18, 2019 at 1:11 PM ‫اسحاق خداپرست سیاهمزگی‬‎ <
issac.kh72_at_gmail.com> wrote:‬

> Hi Dr. Axel
>
> I used VMD for LINUXAMD64, version 1.9.4a12 (December 21, 2017).
> first i made an xyz file. then i used VMD and chnged its format to pdb.
> after that i used topo tools of VMD with this commands:
> {
> topo retypebonds
> topo guessangles
> topo guessdihedrals
> topo guessimpropers
> topo writelammpsdata graphene.data full
> }
> I checked my data for a small structure. the results were the same.
> My reason for wrong dihedrals is that it defines same dihedrals(for
> example):
>
> ID dihedral-type atom1 atom2 atom3 atom4
> 6 3 1 2 4 3 *
> 7 3 3 2 4 3
> 8 1 1 2 3 5
> 9 2 1 2 3 4 *
>
> and
>
> same atom in one dihedral(for example):
>
> ID dihedral-type atom1 atom2 atom3 atom4
> 49 3 *10* 9 11 *10*
>
> *I attached my datafile with this mail.*
>
> Regards
>
> Isaac
>
> ‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ دوشنبه ۱۸ فوریهٔ ۲۰۱۹
> ساعت ۱۸:۱۶ نوشت:‬
>
>> You are making some strong statements here. A) how do you determine, that
>> the dihedrals are guessed "wrong"? B) what does "wrong" mean? Not what you
>> want or not what the algorithm says? C) you don't provide any proof or
>> details of an error, so how can somebody suggest a correction? And finally
>> D) did you provide correct bond information? If yes how?
>>
>> Also, always name the version of vmd and topotools you are using.
>>
>> Axel
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>> On Mon, Feb 18, 2019, 14:31 اسحاق خداپرست سیاهمزگی <issac.kh72_at_gmail.com
>> wrote:
>>
>>>
>>>
>>> Hi
>>> I used topo tools for writing lammps datafile. But this tools makes some
>>> wrong dihedrals. Is there any way to fix this error?
>>> Thanks
>>> Isaac
>>>
>> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.