AMBER Archive (2001)

Subject: box size

From: tianxiao young (txyoung_at_hotmail.com)
Date: Wed Aug 15 2001 - 23:31:40 CDT

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Dear Ambers,

I used constant pressure flag to perform sander_classic calculations.
Counterions(50Cl-+50Na+) were added to increase the concentration. After
1000ps simulation time, the box size decreased from the original
32AA*32A*32A to 25A*25A*25A.

I would like to know whether the compressed box size has any significant
influence on the calculated results, especially on the hydration water
numbers around the solute. Is it possible to keep the box size constant?
Your help will be greatly appreciated.

Best wishes.

Tianxiao YANG

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