Dear Amber users,
I am trying to do a nmr refined MD simulation. Minimization was done for
the system without any error. When doing MD with the protocol
simulated annealing protocol, 20 ps
&cntrl
nstlim=20000, nscm=1000, pencut=-0.001, nmropt=1,
ntpr=200, ntt=1, ntwx=200,
cut=15.0, ntb=0, vlimit=10,
/
&ewald
eedmeth=5,
/
#
#Simple simulated annealing algorithm:
#
#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
value2=600., /
&wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
value2=100.0, /
&wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
value2=0.0, /
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
value2=0.4, /
&wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
value2=4.0, /
&wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
value2=0.05, /
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
value2=1.0, /
&wt type='REST', istep1=3001,istep2=20000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=newRSTA
I got the following message after runnung MD for only 1.6ps
Frac coord min, max: 0.15981055968035968 1.0005435873364954
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.
There is no restart file generated . How will I solve this error.
I put nscm=1000 after going through some former messages, but getting the
same message. If anybody knows , please help out me.
Thank you,
Maya
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Received on Fri Dec 13 2019 - 10:00:02 PST
