I am heating up my system from 0 through 300 K with following input
Initial heating and equilabration
&cntrl
imin=0, irest=0, ntx=1,ig=-1,
nstlim=100000, dt=0.001, ntc=1,
ntpr=100, ntwx=10,
ntr=1, restraint_wt=1, restraintmask=':1-356',
cut=16, ntb=0, igb=0,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=300.0,
/
and output seems like:
.
.
vlimit exceeded for step 562; vmax = 24.7125
vlimit exceeded for step 563; vmax = 22.4023
vlimit exceeded for step 564; vmax = 23.9687
vlimit exceeded for step 565; vmax = 22.1532
vlimit exceeded for step 568; vmax = 27.0609
vlimit exceeded for step 570; vmax = 20.6966
vlimit exceeded for step 571; vmax = 21.8889
vlimit exceeded for step 572; vmax = 21.7495
vlimit exceeded for step 573; vmax = 20.7287
Frac coord min, max: 0.196308421329304 1.00107883142068
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
what could be wrong with the system? velocity limits are being exceeded on
most of the steps.
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Wed Oct 03 2012 - 06:30:03 PDT
