AMBER Archive (2005)

Subject: AMBER: why the dipeptide always moving out the virtual box

From: Li Su (suli_at_msu.edu)
Date: Mon Jun 13 2005 - 16:40:47 CDT

Dear amber users,
 I'm simulating alanine dipeptide in vaccum using sander, but everytime
after around 350 ps, it stops and tells me the "The system has extended
beyond the extent of the virtual box. Restarting sander will recalculat a
new virtual box with 30 Angstroms extra on each side, if there is a restart
file for this configuration." The I use the rst file to restart , but after
about the same period the same problem happens. And the following is my mdin
file:
In-vacuo
&cntrl
 imin = 0,
 ntb = 0,
 igb = 0,
 ntf = 3,
 ntc = 3,
 ntpr = 100,
 ntwx = 100,
 ntt = 3,
 gamma_ln = 1.0,
 tempi = 300.0,
 temp0 = 300.0,
 nstlim = 1000000,
 dt = 0.001,
 cut = 12.0
/
If you know what is the cause, Please e-mail me back. Thank you in advance.

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