Hello
I am trying to simulate a system of dimer molecules in the gas phase. When I turn off the periodic boundaries with ntb=0 it will work but every so often (100-500 ps) it dissociates and I get the error:
NSTEP = 82000 TIME(PS) = 164.000 TEMP(K) = 474.01 PRESS = 0.0
Etot = 35.8464 EKtot = 107.3817 EPtot = -71.5353
BOND = 20.8605 ANGLE = 75.8173 DIHED = 41.7257
1-4 NB = 20.8793 1-4 EEL = -82.8782 VDWAALS = 2.7036
EELEC = -150.6434 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
Frac coord min, max: 0.236659570259939 1.00005584928049
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
Is there any way to define a rigid boundary?
If I use ntb=1 Then I must make the box much larger and then dissociated molecules are less likely to re-associate.
Thank You
Cody Covington
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Received on Tue Jan 26 2016 - 13:30:02 PST
