VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 19 2019 - 01:59:57 CST

One more question. Which force field do you want to use with the resulting
data file?

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 Tue, Feb 19, 2019, 07:54 اسحاق خداپرست سیاهمزگی <issac.kh72_at_gmail.com
wrote:
> Dear Axel
>
> I can make graphene with VMD but I want to make a graphene-oxide .so i
> wrote a c++ programm which make a GO .xyz file. then i used VMD to make
> it's .pdb file and at the end i used topo tools as i said before.
>
> now i attached .xyz and .pdb files that i used.
>
> Regards
>
> Isaac
>
>
> ‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ دوشنبه ۱۸ فوریهٔ ۲۰۱۹
> ساعت ۲۲:۴۴ نوشت:‬
>
>> 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.
>>
>