AMBER Archive (2009)
Subject: [AMBER] MMGBSA
From: Zhongjie Liang (zjliang_at_mail.shcnc.ac.cn)
I am calculating the free energy (including entroy) of 100 structures,
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 2.4098E+19 H10 4716
BOND = 9543232.3761 ANGLE = NaN DIHED =
VDWAALS = ************* EEL = 1012.6342 HBOND =
1-4 VDW = ************* 1-4 EEL = -1918.5531 RESTRAINT =
Frac coord min, max: -16959209342929.1 16959209342930.8
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.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
I wonder what exactly the restart file is , and how to restart the program.
Thanks for any suggestion!