my equil.in file contains the following parameters :
cntrl
! MOLECULAR DYNAMICS
nstlim=2000000, ! Number of MD-steps to be performed.
dt=0.002,
ntx=5, ! read coordinates and velocities from the restart file
irest=1, ! this is not a simulation restart
ntpr=50, ! print energy every 100 steps
!respa=2, ! evaluate forces every step
ntwr=500, ! write restart file (.restrt) every 500 steps
ntwx=500, ! save coordinates every 500
ntxo=2, ! generate binary amber trajectory (.nc file)
ioutfm=1, ! generate binary amber trajectory (.nc file)
ntb=0, ! no PBC with GB solvent
igb=8, ! use the optimized GBn implicit solvent model (ibg=8)
(better than simple GB [igb=1] or OBC[igb=2,5], although less tested)
saltcon=0.15, ! salt concentration
rgbmax=15,
! TEMPERATURE CONTROL
temp0=310.0, ! reference temperature at which the system is to be
kept, if ntt 0
ntt=3, ! Use Langevin thermostat.
gamma_ln=1, ! Damping coefficient for Langevin dynamics in ps - 1.
tautp=0.5, ! Time constant, in ps, for heat bath coupling for the
system, if ntt = 1
! BOND CONSTRAINTS
ntc=2, ! bonds involving hydrogen are constrained with SHAKE
tol=1.0e-8, ! Relative geometrical tolerance for coordinate
resetting in shake
! ELECTROSTATICS & VDW
ntf=2, ! ommit force evaluations for bond interactions
involving H-atoms
cut=999.0, ! Cut-off for vdW and electrostatic interactions.
/
~
~
~
my equil.out file shows the following temperature range :
NSTEP = 2000000 TIME(PS) = 5000.000 TEMP(K) = 7.74
PRESS = 0.0
Etot = 42.0257 EKtot = 25.0931 EPtot =
33.0569
BOND = 14.0995 ANGLE = 21.6915 DIHED =
13.4789
1-4 NB = 7.8585 1-4 EEL = 25.7094 VDWAALS =
23.2774
EELEC = 94.9245 EGB = 102.3078 RESTRAINT =
0.0000
------------------------------------------------------------------------------
as you said to check the equilibration steps.
it is also showing some temperature fluctuations.
please help with these .how can I fix this.
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Received on Fri Jun 29 2018 - 12:30:02 PDT
