Have you tried assigning tempi? I didn't see it in the input.
On Mon, Oct 31, 2022, 12:54 PM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> 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 - 11:30:02 PDT
