AMBER Archive (2001)

Subject: water molecules in a periodic box

From: Giulio Rastelli (giulio_at_caesar.unimo.it)
Date: Mon Aug 06 2001 - 12:03:41 CDT

> I am using sander6 w PME to carry out MD of a solute
> into a periodic box of water, and I noticed that the water
> molecules are spread at the boundaries, and the box is
> not well defined in shape. Is this a normal behaviour?...
> I've seen that the box dimensions are read correctly by sander,
> i.e. they are not the dimensions of the topology file but those of
> the inpcrd file (shrinked after a density adjustment)
>
> Thanks in advance
>
>
> Giulio Rastelli
> Dipartimento di Scienze Farmaceutiche
> Universita di Modena e Reggio Emilia
> Via Campi 183
> 41100 Modena - ITALY
> -------------------------------------
> tel 0039-059-2055145
> fax 0039-059-2055131
> -------------------------------------
>
>