AMBER Archive (2002)

Subject: Re: Q: waters in NPT & periodic boundary condition

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 14 2002 - 11:45:46 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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