On Thu, Jun 28, 2018, 11:37 PM Chhaya Singh <chhayasingh014.gmail.com>
wrote:
> Hi
>
> Thank you for the information.it provided be a clear idea about the issue
> that I was facing.
> So now I have 1300 atoms in my system but during equilibration, I am
> facing a lot, temperature fluctuations of +/- 7-8 K.
> How to fix this. Can you help me with this.
> myheat.out file contains this :
>
>
> NSTEP = 500000 TIME(PS) = 1000.000 TEMP(K) = 8.07 PRESS
> = 0.0
> Etot = 47.1008 EKtot = 26.1566 EPtot =
> 38.4995
> BOND = 14.3809 ANGLE = 22.0068 DIHED =
> 12.5757
> 1-4 NB = 7.7741 1-4 EEL = 25.8777 VDWAALS =
> 32.7942
> EELEC = 65.3376 EGB = 63.4992 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
>
> --------------------------------------------------------------------------------
>
> my heat.in file contains the following parameters:
>
>
> &cntrl
> ! MOLECULAR DYNAMICSE
> nstlim=500000, ! Number of MD-steps to be performed.
> dt=0.002,
> ntx=1, ! read coordinates and velocities from the restart file
> irest=0, ! this is not a simulation restart
> ntpr=50, ! print energy every 50 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 traj
> ectory (.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
> tempi=0.0, ! initial temperature
> temp0=310.0, ! reference temperature at which the system is to be
> kept, if ntt 0
> ntt=3, ! Use Langevin thermostat.
> gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
> tautp=1.0, ! Time constant, in ps, for heat bath coupling for the
> system, if ntt = 1
>
> ! PRESSURE CONTROL
> ! ntp=0, ! do not use pressure coupling
>
> ! 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
> "heat.in" 48L, 2499C
>
>
> Thanks
>
>
>
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Received on Thu Jun 28 2018 - 11:30:02 PDT
