[ifpsc] Re: Forcefield database proposal resulting from our

Huai,

Thanks for your response.  My preference would be to discuss the
forcefield database ideas on the discuss-ifpsc@xxxxxxxxxxxxx public
email list (it's nominally public, but right now it is the IFPSC
steering team...though I took the liberty of adding you).  That way,
other IFPSC folks who are interested can be involved in the discussion.

I take your point that existing force fields are too diverse to be used
together.  My vision isn't of a database with all the parameters (or
even most of them) are suitable for use with each other.  I imagine
something more heterogeneous including the major force fields (AMBER,
Gromos, TraPPE, COMPASS, TEAM, etc.) there as well as many much more
limited models (maybe only applicable to one molecule).  Though general
and transferable is the ideal, both types (general/transferable and not)
are part of the literature and both have some usefulness.  Admittedly,
I'm sure I don't fully appreciate how difficult it would be to integrate
such a diverse set of force fields into a database that would be useful.

Jonathan

____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 300E
Midland, MI 48674  USA
Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: jmoore2@xxxxxxx

-----Original Message-----
From: Huai Sun [mailto:huaisun@xxxxxxxxxxx] 
Sent: Sunday, September 09, 2007 1:10 AM
To: Moore, Jonathan (J)
Subject: Re: [ifpsc] Forcefield database proposal resulting from our 

Dear Jonathan,

First of all, thanks a lot for your kind email and suggestions. I just
came 
back from vacation, that's why I am slow in response. We are studying
all 
the comments and suggestion received and revising our proposal.

Generally speaking, I appreciate the idea of open, user-supported
databases. 
My concern is that existing force fields are too diversified to be put 
together. Basically, the atom types are named differently, the
parameters 
for the same types of interactions (e.g. C-C-C angle terms) are
differrent 
from different developers. The consequence is that these parameters can
be 
used only for the systems (molecules) they are designed for; for most 
industrial uses, the coverage is not enough.

Based on my experiences, in order to make a high quality and
transferrable 
force field, the parameters must be internally consistent. The same 
difinition of atom types and same protocol of parameterization must be
used.

We can create a force field repository that users can put and get
freely. To 
create such a website and database does not cost too much, we can do it
on 
our own expenses. Meanwhile, we are developing consitent and extensible 
databases from literature and from our own work. For that we have and
will 
continue put in a lot of efforts. However, I believe only the letter can

solve the industrial needs. We are working on it currently, by the time
of 
next IFPSC meeting in Novermber, I hope to show a protocol. For
continuring 
developments and supports we must find someway to support this effort.

At this point, in order to find the best way to go, I am discussing the 
ideas with folks I know. 

Best Regards,

Huai


----- Original Message ----- 
From: "Moore, Jonathan (J)" <JMoore2@xxxxxxx>
To: <ifpsc@xxxxxxxxxxxxx>
Cc: <huaisun@xxxxxxxxxxx>
Sent: Wednesday, August 08, 2007 3:36 AM
Subject: RE: [ifpsc] Forcefield database proposal resulting from our


> Fiona,
>
> I think Huai's proposal is, in general, excellent.  If it is realized,
I
> think it will be a great help.  I hope he will be successful.
>
> However, my enthusiasm is significantly dampened by its fee-based
> nature.  I would be much more interested in a plan that required
> monetary support to get it up and running (building the database, the
> website, etc.) but then transitioned to a free and open resource where
> the users (rather than Huai's group alone) were responsible for
> uploading parameters, validation studies, etc.  The forcefield
> developers themselves would take on the small burden of uploading
their
> parameters, etc. via a user-friendly interface provided by the system.
> When parameters aren't available or aren't adequate, the user could be
> directed to options for consulting or software purchase, but I'm more
> interested in a database system that is open and maintained by the
> community than one that is proprietary and only accessible after
> payment.
>
> That direction (in the spirit of Wikipedia, Free/Libre/Open-Source
> Software, open access in science, etc.) is what I'd like to promote.
>
> Jonathan
>
>
> Jonathan
>
> ____________________________
> Jonathan Moore, Ph.D.
> Research and Engineering Sciences - New Products
> Core R&D
> The Dow Chemical Company
> 1702 Building, Office 300E
> Midland, MI 48674  USA
> Phone:  (989) 636-9765
> Fax: (989) 636-4019
> E Mail: jmoore2@xxxxxxx
>
> -----Original Message-----
> From: ifpsc-bounce@xxxxxxxxxxxxx [mailto:ifpsc-bounce@xxxxxxxxxxxxx]
On
> Behalf Of Fiona Case
> Sent: Tuesday, August 07, 2007 12:55 PM
> To: ifpsc@xxxxxxxxxxxxx
> Cc: huaisun@xxxxxxxxxxx
> Subject: [ifpsc] Forcefield database proposal resulting from our
>
> Hello,
>
> Here is the proposal from Huai Sun that I mentioned at our committee
> meeting. I think this is a great idea. I have at various times in my
> career
> spent many days/weeks searching for force field parameters and typing
> them
> into files - and I occasionally had to abandon projects because good
> parameters were not available. If webDDF had been available I would
have
>
> certainly used it!
>
> Huai would be very interested to receive feedback from the IFPSC
> committee.
> His email is
>
> "Huai Sun" <huaisun@xxxxxxxxxxx>
>
> Best wishes
>
> Fiona
>
> _________________________________________________________________
> Learn.Laugh.Share. Reallivemoms is right place!
> http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us 
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