On Sat, Jun 30, 2018, 12:56 AM Chhaya Singh <chhayasingh014.gmail.com>
wrote:
> 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 - 15:00:02 PDT
