AMBER Archive (2004)

Subject: AMBER: solute leaving PBC box

From: opitz_at_che.udel.edu
Date: Thu Oct 07 2004 - 16:24:47 CDT

('binary' encoding is not supported, stored as-is) Dear Amber Community,

I am running MD in a periodic box, with the following input:
&cntrl
 imin=0, irest=1, ntx=5,
 iwrap=1,
 ntb=2, ntp=1, pres0=1, taup=1.0
 ntf=1,
 igb=0,
 ntr=0, cut=12,
 ntt=1, tempi=300, tmp0=300, tautp=1
 nstlim=2600000, dt=0.01, t=400,
 ntpr=1000, ntwx=1000, ntwr=1000
&end
At the end of this I took a look at my simulation, and my solute (the
molecule of interest), has migrated through the box to one of its
corners. Parts of the molecule are sticking out of the box, and aren't
imaged back into the box.
Does this affect the molecule behavior? If so how could i prevent it from
leaving the box?
Please help.

Best Regards,

Armin

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