Periodic Box

From: John Finke <>
Date: Fri 7 Feb 2003 16:25:10 -0800 (PST)


I have an AMBER problem which I am having some difficulty,

I am using sander_classic to run MD on 2 separate peptide fragments and
intend to use a periodic box to keep them close to one another and avoid
them flying away from one another.

I have followed the tutorial examples as much as possilble to create a
periodic box (with no waters). The dimensions of this box are listed at
the last line of the topology parmtop file.

  0.90000000E+02 0.34297554E+02 0.33792557E+02 0.34400002E+02

I don't know what the first number is but the next three are the x, y, z
dimensions of the box.

In any event, it appears that sander is ignoring the box as the 2 peptides
simply end up flying away from each other (at distances farther than the
box). I have made sure my imput &cntrl parameter specifies ntb = 1 (which
should be sufficient, right?)

If anyone has had experience using periodic boxes with sander_classic, I
would appreciate any advice they could give me.



John Finke
Received on Fri Feb 07 2003 - 16:25:10 PST
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