VMD-L Mailing List

From: MyLinkka (mylinkka_at_gmail.com)
Date: Fri Jan 15 2010 - 21:54:19 CST

Hi, Alex,

Indeed we have different understanding of improper.
To me it's nothing very different from the dihedral.
I think that's also explains why most books and tutorials
about MD draw pictures like I referred to. Or vice versa.
However, from quantum mechanics point of views, the sticks
connecting atoms (so-called bond in force field) does not
really exist, let alone the angle, dihedral and improper.
Then, indeed, we have to guess everything in order to use
force fields, because most force fields contain those four
terms. On the other hand, molecular structure file usually
contains only positions or position+bonding, like car/mdf,bgf,
because these two things really define the topology of a
molecule. (or we can say the topology people want. )
However, this is not enough to meet the requirement of a
force field, we still need to provide angle, dihedral,
improper or maybe more depending on the force fields.

The point is, most force fields define parameters based on
bonding information (or topology). For example, two consecutive
bonds form an angle; three form a dihedral; three bonds sharing
a common center atom form an IMPROPER (some call it out-of-plane).
by this common definitions, improper does not need to be guessed
it can be derived or searched base on the bonding information.
We can define more distinct structures and names, but those are
not needed by force fields normally. The essential point here
is we do 'guess' for these geometric information for the force
fields, or they are meaningless. Then, why not do it following
the most common definition of force fields. In this sense, tools
like msi2lmp do not just do translation, they build angle, dihedral
and improper geometric information then map the force field
parameters to them. Please have a look of some force field files
you can easily understand this. The definitions of improper angle in
different force fields are essentially the same. This way people don't
really have to specify the parameters manually.

Back to topotools, if some tools can export bond, angle, dihedral
and improper explicitly, it is very convenient for users to assign
force field parameters, although it can be not necessary. see the
lammps command improper_style you will understand this. Or this
automatically typing and force field parameter mapping will automatically
done by some sophisticated software like Materials Studio.

Thank to the discussion. It makes me get better understanding of
the relationship of topology and force field.

Ting

Axel Kohlmeyer wrote:
> On Sat, 2010-01-16 at 00:53 +0100, MyLinkka wrote:
>
>> Hi Alex,
>>
>
> dear ting,
>
>
>> To be honest, your explanation of improper angles is really new to me.
>>
>
> o dear. how long have you been using MD? have you never looked
> at a paper describing the implementation a classical force field?
>
>
>> But I still can't get your idea exactly. From the picture I showed you
>> in previous post, it seems improper angle is really just a geometric
>>
>
> you should not infer from an image, but know from
> its actual definition and use.
>
>
>> definition,related to nothing else. If this is not true, could you
>> please give an example what kinds of information other than bonding
>> are NECESSARY in order to get impropers? (Let's always suppose the
>> bonds are known.)
>>
>
> actually bonds are note really required for impropers. the whole
> point of improper angle interactions is to ensure a geometry that
> would otherwise not be possible to achieve with plain angles and
> dihedrals. for example to keep systems of conjugated double bonds
> planar. to decide whether this is the case, you need to know more
> than just bonds and atoms, hence you cannot guess them.
>
> cheers,
> axel.
>
>> Ting
>>
>>
>>