Dear Amber users,
I didn't set any volume and pressure control when I ran my production run.
What is the default ensemble in this situation?
Here is my prod.in file:
A simulation for common production-level simulations
&cntrl
imin=0, ! No minimization
irest=1, ! This IS a restart of an old MD simulation
ntx=5, ! So our inpcrd file has velocities
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=300.0, ! Target temperature
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=12500000, ! 50 ns
dt=0.004, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=25000, ! Print energies every 100000 steps, 100,000*0.002 =
200ps
ntwx=25000, ! Print coordinates every 100000 steps to the trajectory
ntwr=25000, ! Print a restart file every 100000 steps (can be less
frequent)
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
! Set water atom/residue names for SETTLE recognition
watnam='SOL', ! Water residues are named WAT
owtnm='OW', ! Water oxygens are named O
hwtnm1='HW1'
hwtnm2='HW2'
&end
Thanks for any reply!
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Received on Fri Jul 28 2023 - 09:00:02 PDT
