Hi Chhaya
What they are all trying to say is that a fluctuation in Temperature around
the set value is absolutely normal. This also applies to other variables
such as pressure.
For example have a look at some tutorials, e.g.
http://ambermd.org/tutorials/basic/tutorial3/section6.htm where you'll
clearly see that with rising temperature also comes more fluctuation. The
link shows the temperature curve during the heating stage, the more the
temperature rises, the more it will fluctuate around the average
temperature (which you define in the input file).
So you shouldn't worry about the temperature not being 'constant', the
average temperature however should be rather constant.
Hope this helps
Charles-Alexandre Mattelaer
Op vr 29 jun. 2018 21:27 schreef Chhaya Singh <chhayasingh014.gmail.com>:
> 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 Sat Jun 30 2018 - 06:00:02 PDT
