AMBER Archive (2007)

Subject: AMBER: A question related with periodic boundary condition

From: Jun Liu (junliujun_at_gmail.com)
Date: Tue Sep 18 2007 - 20:48:22 CDT

Dear all,

I have met a problem on using the periodic boundary coundition.

I prepared a file (nef.pdb) which contains the coordinates (x,y,z) of a
FCC(face center cubic) structure. The interaction between particles are the
LJ-potential.

nef = loadpdb nef.pdb
set nef box 14.2223
saveamberparm nef nef.top nef.xyz

Then I set "ntb = 1" and "cut = 6.11". Before I run the MD simulation, I
checked the force first. I noticed that the forces are very different if a
displacement of every particle in the box was put in the file nef.pdb, i.e,
(x-a, y-a, z-a), where a is the displacement for each particle, i.e. a
translational move of the initial box. However, if the PBC is applied, the
displacement a will not affect the force at all. Does anyone have a clue on
what wrong with what I did?

Thank you very much!

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