AMBER: How to manually adjust periodic boundary conditions (PBC)

From: Chin, Keith B <>
Date: Wed, 19 Nov 2008 11:58:41 -0800


I was wandering if anyone know how to adjust periodic boundary conditions in sander *crd and *top files for MD.

Suppose rather than a box lattice, I wish to apply PBC for hex lattice, where a=4.516, b= 4.516, c = 7.435, alpha = 90, beta = 90, gamma = 120.

I tried using the xleap SetBox cmd to assign PBC parameter close to my hex parameters, and then manually adjust the gamma angle to 120 instead of 90 in the last line of the *.crd file. However, this gave me an error of when executing the MD, which indicates that my PBC parameters is still too small for my lattice.

Here's the error in my md output file:

 parameter skinnb+cutoffnb: (nonbond list cut) has value 0.12000E+02
 This is outside the legal range
 Lower limit: 0.00000E+00 Upper limit: 0.58665E+01
 Check ew_legal.h

Only when I expand my PBC parameters way beyond my original lattice size does the MD executes completely, but obviously it'll provide bad results, especially for density.

Any advise on how to do this OR where I can find more info on resolving this issue.

Thanks in advance.
Keith Chin
Electrochemical Technologies Group
Office: (818) 354 - 4051

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Received on Fri Dec 05 2008 - 16:03:30 PST
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