AMBER Archive (2004)

Subject: AMBER: atoms out of bounds

From: Balvinder Singh (
Date: Thu Oct 07 2004 - 16:27:45 CDT

I am running a dynamics calculations using amber7 on a protein neutrilized
by one ion. I have minimized the system with DRMS 0.00001 with distance
dependent dielectric. I have equilibrated the system for 500 ps and
raising the temperature (from 0K to 300K) in smaller steps of 30K/50 ps.
Visual inspection of protein at the end of equilibration shows that IB has
moved a bit far away from the protein (nearest atom of prtein to IB is 64
A distance). While subjecting the system to production run, following
error occured.

Frac coord min, max: -8.20798303E-07 0.879446721
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

The above error also appears to be related to that only whereby the IB is
moving further away from the protein and resulting in atoms out of bounds.
The protein is intact. I am sure that restarting it is not going to solve
the problem as IB may move further away as simulation progresses.

What are the possible reasons for IB drifting away? How to overcome this

Latest input of equilibration step (It was performed in steps):

    imin=0, irest=1, ntx=5, ntb=0, cut=50,
    ntr=0, tempi=300, temp0=300, ntt=1,
    tautp=1.0, dielc=4,
    ntpr= 500, ntwx=1000, ntwr=1000,

Input for production run:

    imin=0, irest=1, ntx=5, ntb=0, cut=50,
    ntr=0, tempi=300, temp0=300, ntt=1,
    tautp=0.5, dielc=4
    ntpr= 5000, ntwx=10000, ntwr=10000,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to