AMBER Archive (2000)

Subject: periodic boundary conditions

From: Pascal Bonnet (pascal_at_qorws1.uab.es)
Date: Mon Oct 09 2000 - 13:58:11 CDT

        dear all,

When I display the result from a simulation run (trajectory file) of a
molecule dimer, I can see that one molecule is outside the water
molecules box like an image .

For example I obtain:

first of the simulation: X1 is one molecule , X2 is the other molecule
of the dimer

_________________
| |
| X1 |
| X2 |
|________________|

During the simulation the dimer is :

__________________
| |
|X1 |
| |X2
|_________________|

Do the interaction energies could be the same than:

___________________
| |
|X1 |
|X2 |
|__________________|

using the periodic boundary conditions ????

Thanks

PB 

-- 
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Pascal Bonnet 	pascal_at_qorws1.uab.es

Unitat Quimica Organica   and	   Institut de Chimie Organique et Analytique
Facultat de Ciences 		   UFR Sciences - UPRES-A 6005
Universitat Autonoma de Barcelona  Rue de Chartres - BP 6759
08193 Bellaterra (SPAIN)	   45067 ORLEANS CEDEX 2 - France		   
Tel: 34935811266		   Tel: 0238494577  	    
Fax: 34935811265
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