[MMTK] shake

Patrick Fleming pat.fleming at jhu.edu
Thu Nov 4 16:15:35 CET 2004


Just to be sure I understand - the following code seems to give me the 
correct distance constraints list. That is H1-O, H2-O, H1-H2 are specified.

Any problems with doing it this way?

---------------------------------------------------------
# SHAKE waters
water = Collection()
for object in universe:
     try:
         is_water = object.type.name == 'water'
     except AttributeError:
         is_water = 0
     if is_water:
         water.addObject(object)

water.setBondConstraints()
----------------------------------------------------------


hinsen at llb.saclay.cea.fr wrote:

> On 04.11.2004, at 02:35, Patrick Fleming wrote:
> 
>> How does one specify distance restraints during MD to implement the  
>> equivalent of SHAKE for water?
> 
> 
> For everything:
> 
>     universe.setBondConstraints()
> 
> For one molecule:
> 
>     molecule.setBondConstraints()
> 
> For anything in between, use a collection object to group the molecules.
> 
> Since water is defined with an H-H-bond, this will keep water molecules  
> completely rigid.
> 


-- 
Patrick Fleming, Ph.D.
The Johns Hopkins University
Department of Biophysics
201 Jenkins Hall
3400 North Charles Street
Baltimore, MD 21218

Tel: 410-516-7654
Fax: 410-516-4118




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