Dear all AMBER expert,
I'm an new user in AMBER, and hence, I have a lot of downs when
choosing parameter for particular ensemble.
I want to run NVE simulation, the paramaters I set are following:
prod
&cntrl
imin=0, # turn off minimixation = md
irest=1, ntx=5, # restart calculation, requires velocities in
coordinate input file
nstlim=5000000, # number of MD steps
dt=0.002, # time step (ps)
ntc=2, # flad for SHAKE, bonds involvimg hydrogen are contrained
ntf=2, # force evaluation, bond interactions involing H-atoms omitted
cut=14.0, # specific the nonbonded cutoff, in Angstroms
ntb=1, # periodic boundary, constant volume
taup = 0.1, # pressure relaxation time (in ps)
ntpr=5000, # every ntpr steps energy information will be printed in
human-readable form to mdout file
ntwx=5000, # every ntwx steps the coordinates will be written to mdcrd file
ntt=0, # pure Newtonian dynamics
ig = -1 # change the random number seed from the default on every MD restart
temp0=300.0, # reference temperature
/
Would you mind telling me whether the parameter is suitable for NVE
ensemble? If I choose taup = 0.1, does my simulation change to NPE or
NPV?
Do I need to set the ntp=0 and tempi=300.0? How about iwrap = 1,
tol=0.000001 (SHAKE) and dsum_tol to 10**-6 ?
Thank you in advance.
Regards,
Binh
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Received on Thu Apr 04 2013 - 02:00:03 PDT
