Re: Q: waters in NPT & periodic boundary condition

From: David A. Case <>
Date: Wed 14 Aug 2002 09:45:46 -0700

On Wed, Aug 14, 2002, Masaki Tomimoto wrote:
> I have done MD simulation with a periodic boundary condition and NPT
> system. The protocols is almost the same as those in a AMBER tutorial of
> DNA. After MD simulation was done, I took a look at its final snap shot
> by using ptraj and ambpdb commands. The solvent box fairly changed its
> shape. Some parts caved in, Others swelled. Furthermore, some waters
> were far apart from the distorted solvent box.
> My question is
> (1) Is this phenomena normal in NPT system?
> (2) Is something wrong?
> (3) If I use NVT system, shape of the solvent box will be kept as a
> rectangular parallelepiped?

What you see is normal. You need to use the "image" command in ptraj to
re-translate your waters back to the primary unit cell. Then the box shape
will "look" correct. See the documentation on "image" at p. 202 of the
Users' Manual.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Wed Aug 14 2002 - 09:45:46 PDT
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