Hello Amber users
i m using Amber 9 to carry out implicit simulation of a protein molecule
containing around 3000 atoms but i found that the mini. or equi. in implicit
solvent is much slower than the mini or equi.in the explicit solvent , i
think for this much no of atoms the simulationshud be faster the explicit ,
please tell me the reason for this unusual behaviour
following are the input files i m using :
for mini.
imin=1,igb=2,cut=300.0,maxcyc=500,ncyc=250,ntr=1,ntb=0
for equi.
imin=0,igb=2,cut=300.0,ntr=1,ntb=0,nstlim=20000,dt=0.002,ntc=2,ntf=2,
tempi=10.0,temp0=300.0,ntt=1,tautp=2.0,ntp=0,ntpr=100,ntwx=0
thanks
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Received on Wed Apr 25 2007 - 06:07:13 PDT
