AMBER Archive (2002)

Subject: Q: waters in NPT & periodic boundary condition

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Wed Aug 14 2002 - 11:06:15 CDT

Hi All,

   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?

Thank you in advance

Masaki Tomimoto
Sr. Scientist
Structural GenomiX Inc.