Dear AMBER Community,
Is it normal for a system to take ~3 ps to reach the target temperate when generating anew the velocities?
I normally don’t print out every ps, but for a fast-growth or morphing thermodynamic integration (TI) simulation, that’s exactly what I did last night. I noticed the temperature rose from 0 to 300 K over the first 3 ps. The same behavior occurred in just an NPT simulation without changing the lambda variable (clambda) from zero.
Below is my input if it helps. (I’m very obsessive about knowing keywords!)
&cntrl
ig=-1, ! Random seed (=-1, get a number from current date and time)
irest=0, ! Flag to restart the simulation
ntx=1, ! Initial condition (=1, read coord. but not veloc. from inpcrd file)
dt=0.001, ! The time step in picoseconds
nstlim=20000, ! Number of MD steps to be performed
ntt=3, ! Temperature scaling (=3, Langevin dynamics)
gamma_ln=2.0, ! Collision frequency of the Langevin dynamics in ps-1
temp0=300.0, ! Reference temperature
ntp=1, ! Constant pressure dynamics (=1, isotropic position scaling)
barostat=2, ! Barostat to control the pressure (=2, Monte Carlo)A
pres0=1.0, ! Target pressure (1 bar)
taup=1.0, ! Pressure relaxation time in ps
ntb=2, ! Boundaries (=2, constant pressure)
igb=0, ! GB model (=0, explicit solvent)
cut=10.0, ! Cutoff
ntc=2, ! SHAKE constraints (=2, hydrogen bond lengths constrained)
ntf=1, ! Force evaluation (=2, hydrogen bond interactions omitted)
ntr=0, ! no positional restraints
nmropt=1, ! To vary target temperature below
icfe=1, ! Turn on free energy calcs
ifsc=1, ! Use softcore potentials
scalpha=0.5, ! alpha parmaeter in vdW decoupling
scbeta=12, ! Å^2; scaling parmaeter for softcore electorstatics
gti_cut=1, ! Normal non-bonded cuttoff not applied among softcore
gti_chg_keep=1, ! Do not neutralize charges on softcore atoms
gti_lam_sch=0, ! Do not use lambda scheduling
gti_ele_sc=0, ! Do not use smoothstep function for electrostatics
gti_vdw_sc=0, ! Do not use smoothstep function for vdW interactions
gti_add_sc=1, ! Scale 1-4 non-bonded terms between common and softcore by lambda
gti_bat_sc=0, ! Do not scale bonded terms between common and softcore by lambda
gti_output=0, ! Default output
gti_cpu_output=1, ! Combine and output lambda-derivative terms for all TI regions
clambda=0.0, ! Value! Value of perturbation parameter
dynlmb=0, ! Increment clambda every ntave steps in single morphing simulation
ntave=100, ! Number of steps for each clambda in single morphing simulation
klambda=1, ! Exponent in perturbed potential function
tishake=1, ! Normal use of SHAKE
noshakemask='.3630-3644,8047-8068,4389-4410,8813-8827',
timask1='.3630-3644,8047-8068',
timask2='.4389-4410,8813-8827',
scmask1='.3630-3644,8047-8068',
scmask2='.4389-4410,8813-8827',
crgmask= , ! Set to zerggo charges on mask
ti_vdw_mask= , ! Set to zero vdW for mask
logdvdl=0, ! Print dv/dl info
ntwr=50, ! Restart file written every ntwr steps
ntwx=50, ! Trajectory file written every ntwx steps
ntpr=1, ! The mdout and mdinfo files written every ntpr steps
ntxo=2, ! Write NetCDF coordinate file
ioutfm=1, ! Trajectory file format (=1, Binary NetCDF)
iwrap=0, ! Translate water molecules into the original simulation box
/
&wt type='DUMPFREQ', istep1=100 /
&wt type='END' /
DISANG=InterSubunitRestraints.rst
DUMPAVE=InterSubunitRestraints_TIprep.dat
Best,
Matthew
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Received on Mon Oct 31 2022 - 11:00:03 PDT
