Re: [AMBER] Simulating a periodic System about Molecular Crystal

From: David A Case <>
Date: Mon, 6 Jun 2011 07:45:45 -0400

On Mon, Jun 06, 2011, hanlu0366 wrote:
> In my process , I did follow the Tutorial A13,but I come across another
> problem that the software let you to set a box when you set ntb = 1 . I
> want to ask whether the tools which is used to establish the Crystal in
> AmberTools 1.5 make the structure established containing the periodic
> boudary conditions . If they make the structure estabished containing
> periodic boundary conditions ,why the software ask for your setting box
> (ntb=1).

I don't understand your question, but maybe the following information will
help. You need to inform Amber that you will be running a periodic simulation
when you set up the prmtop and inpcrd files, which have information on the
type of unit cell and its dimensions. You also need to set ntb=1 in the
pmemd/sander input file; this may sound redundant, but there are cases where
where one might want to run a non-periodic calculation on a periodic system.


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Received on Mon Jun 06 2011 - 05:00:03 PDT
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