[MMTK] TIP4P water potential in MMTK

pierre-nicholas roy pn.roy at ualberta.ca
Tue Feb 26 17:43:11 UTC 2008


Hi all,

A student and I have implemented TIP4P in MMTK. We did it without
dummy atoms in order to have a proper accounting of degrees of freedom
for our particular application (semiclassical quantum dynamics).
This is done with the chain rule to obtain gradient components on atoms.

We implemented it by modifying the C forcefield example provided by  
Konrad.
To use it, you will need to install the forcefield using the setup.py  
procedure.

I will prepare a tarball containing the following files:
setup.py (to build and install)
MMTK_tip4p_dimer.c (where the gradient components are calculated)
TIP4PdimerFF.py (the interface between C and python)
dynamics.py (a simple script where the dynamics of water clusters is  
studied).

Konrad: where should I send this? On the wiki? How?

I hope this will help.

regards,

pnr

> Hello again,
>
> Is it possible to implement the TIP4P water potential (Jorgensen et  
> al.,
> J. Chem. Phys, 79(2), 926 (1983)) into the Amber force field in MMTK
> instead of TIP3P, which is the standard water potential?
>
> This requires that one must specify charges and force constants for
> hamonic oscillators etc., for points that are not located on atoms,
> which seems not to be possible in MMTK (when reading through the
> "Constructing the Database" section in the MMTK manual)?
>
> Is it possible to construct a water molecule in the database that
> contains a mass-less atom (then one can specify charges for this in  
> the
> database file and force constants in the Amber database)?
>
> Kind regards
> Andreas
>> -


Pierre-Nicholas Roy, PhD
Associate Professor
Department of Chemistry
University of Alberta
Edmonton, AB, Canada, T6G 2G2
http://www.chem.ualberta.ca/~pnroy/
Phone: (780) 492-0317









More information about the mmtk mailing list