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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 28 2018 - 11:30:02 PDT
