VMD-L Mailing List

From: MyLinkka (mylinkka_at_gmail.com)
Date: Fri Jan 15 2010 - 23:25:21 CST

Thanks, Axel, for making the useful tool!
I reserve some of my opinion.

Ting

Axel Kohlmeyer wrote:
> On Sat, 2010-01-16 at 04:54 +0100, MyLinkka wrote:
>
>> Hi, Alex,
>>
>
>
>> Indeed we have different understanding of improper.
>> To me it's nothing very different from the dihedral.
>>
>
> it is not very different from how it is being implemented
> or how you would define it. but they are _very_ different
> in how they are used.
>
>
>> 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.
>>
>
> this is totally irrelevant for our discussion.
>
>
>> 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
>>
>
> the force field indeed contains parameters for all, but
> that again is irrelevant, since they get looked up or
> assigned based on the topology information.
>
>
>> 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.
>>
>
>
>> by this common definitions, improper does not need to be guessed
>> it can be derived or searched base on the bonding information.
>>
>
> in all the topology generating tools that i know of, improper
> definitions are always looked up based on residue or template
> data base. and in several cases impropers were defined between
> atoms that were _not_ bound together in the way you have
> described it. what you described, is only the most common
> form of an improper.
>
> in any case, just create a .psf file with psfgen for example
> and look up the number of dihedrals and impropers, and you'll
> see that there are by far fewer impropers than dihedrals.
> however, given your reasoning, that should not be the case.
> furthermore impropers are explicitly given in charmm force
> field topology files, angles and dihedrals not.
>
>
>> 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
>>
>
> topotools _is_ following the most common way force fields are
> defined. what you are suggesting is uncommon. what you suggest
> is technically the same as to defining additional bond/angle/dihedral
> interactions and then setting all their coefficients to zero.
>
>
>> 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
>>
>
> but this is exactly what i am saying. you cannot guess impropers
> without _additional_ information. in your case you get it from
> the force field database, where distinct atom types contain the
> important information about what kind of structure you have and
> then you can derive whether you need to add an improper interaction.
>
> this is effectively the same as setting them explicitly.
> topotools does not have that information available.
>
>
>> 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.
>>
>
> this is not about parameters, and different force fields
> do have
>
>
>> 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.
>>
>
> for that kind of functionality VMD already has psfgen.
> this is not what i am aiming at.
>
> you have the source code for topotools, feel free to implement
> a guessimpropers functionality still believe you need it. i am
> certain, that you will realize in the process that it is a
> pointless effort. i didn't omit it, because it didn't think
> about it, but rather because it doesn't make sense in the
> context of the other guessXXX functions.
>
> cheers,
> axel.
>
>
>> Thank to the discussion. It makes me get better understanding of
>> the relationship of topology and force field.
>>
>> Ting
>>
>
>