VMD-L Mailing List

From: MyLinkka (mylinkka_at_gmail.com)
Date: Fri Jan 15 2010 - 06:05:53 CST

Hi Alex,

I'm confused. Why you think improper should be that different
from bond, angle and dihedral? It's just a out-of-plane
dihedral involving 4 connected atoms, isn't it?

see Figure 2.at
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html
and
figure here: http://hidra.iqfr.csic.es/man/dlpoly/USRMAN/node50.html
and there clearly show the difference between dihedral and improper, I
think.

and more, the msi2lmp tool shipped with lammps also can produce improper
list
in the output lammps data file. I don't mean to compare them with topotools.
Just hope to make myself clear.

When I write here, I realize maybe there is some misunderstanding.
I didn't mean judge everything from ONLY the atom coordinates!
I know that's automatically done in VMD if the input file has only atom
positions but no bonding information there. What I want to say is
ONCE we have known the bonding info., we can derive angles, dihedrals
and impropers only based on the topology information. We don't have to
guess any more. Of course, not all the force fields has all parameters for
all impropers, or we can think the energy constant is zero.
Or if you say, bond, angle, dihedral or improper can include non-bonded
atoms, then distance based guess may be necessary. But this is not usual.

Ting

Axel Kohlmeyer wrote:
> On Wed, 2010-01-13 at 17:41 +0100, MyLinkka wrote:
>
>> Hi Axel,
>>
>>
>> I can understand to guess impropers just based on
>> atom coordinates is ridiculous. But once the bonds,
>> angles and dihedrals are already provided explicitly
>> or guessed, I think the impropers should also be defined,
>>
>
> no, why?
>
>
>> right? In this case no guess is needed.We can always
>> define an improper with 4 atoms, i,j,k,l, with i the center
>> and j,k,l connecting to i.In principle if the atoms
>> positions and bonds are provided, we can write out all the
>> internal coords. (bond/angle/dihedarl/improper). I don't
>>
>
> with this logic in mind, please explain what would be the
> difference between an improper and a dihedral.
>
>
>> really understand why you say improper must be give
>> explicitly? Could you please explain it further?
>>
>
> have a look at what impropers are used for!
>
> you need to know more about the system and
> the force field to place impropers. there is
> no way to guess them from topology alone. to
> a lesser degree this is true for bonds, angles,
> and dihedrals. this is why i called those subcommands
> _guess_something to indicate some vagueness and
> need to recheck.
>
> cheers,
> axel.
>
>
>> Ting
>>
>>
>> Axel Kohlmeyer wrote:
>>
>>> On Wed, 2010-01-13 at 15:28 +0100, MyLinkka wrote:
>>>
>>>
>>>> Hello, Axel,
>>>>
>>>>
>>> hello ting,
>>>
>>>
>>>
>>>> Will there be a guessimpropers function in this plugin?
>>>>
>>>>
>>> no. never.
>>>
>>>
>>>
>>>> I didn't find it in v1.1 and neither in the todo list in README
>>>>
>>>>
>>> please think about it for a little bit, and then
>>> you should realize that impropers always have to
>>> be given explicitly, or would at least need very
>>> special heuristics for specific cases.
>>>
>>>
>>>
>>>> Thanks for making this useful tool!
>>>>
>>>>
>>> you're most welcome. it has been fun writing it.
>>> i only wish i had more time for working on it. :-(
>>> there is still so much that could be done.
>>>
>>> cheers,
>>> axel.
>>>
>>>
>>>
>>>> Ting
>>>>
>>>>
>>>
>>>
>
>