Dear friends,
I am performing MD with sander_classic to equilibrate a solute
into a periodic box of water. I adjusted the dimensions of the
box by runnging a MD with constraints on the solute, to let
the density increase to about 1. Then, I minimized everything and
I started equilibrating the whole thing. The problem is that
when I do the equilibration, the box dimensions that sander_classic
reads are those of the topology file, and the starting density is
consequently very low (about 0.7). I connot read the box information
using ntx=7 because I don't have velocities in my inpcrd file, as
I am starting MD from a minimization.
Finally, I've seen that sander with PME reads box information
correctly, i.e. from the topology first, and then from the inpcrd
file next, and that box info is present in inpcrd files of minimization.
Is there a way to read the correct box info starting from a minimization
inpcrd file, using sander_classic?
Thanks in advance
Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
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tel 0039-059-2055145
fax 0039-059-2055131
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Received on Tue Jul 31 2001 - 10:39:29 PDT
