[gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition
Romulo Leoncio Cruz Simbron
romulocruzs007 at gmail.com
Mon Jan 2 18:40:15 CET 2017
Hello Gromacs User
I have done a molecular dynamics of no bonded, Lennard Jones of 100
molecules of argon in a box. The steps followed have been:
1. EM
2. NVT-100K
3. NVP - 1 atm
4. Annealing 100k to 25K with NVT and NVP
I have noticed that in the enthalpy diagram the phase transition depends
largely on the number of steep I make, approaching the correct value as it
increases from 1 ns to 100 ns of simulation time (from 500 000 to 50 000
000 steps), dt = 0.002. I would like to know if that behavior is correct or
if my molecular dynamics has an error. Additionally if it is correct, is
there an optimum simulation time value?
On the other hand, the enthalpy of gas to liquid, seen in entalpia.xvg, is
two orders of magnitude greater than the value of the enthalpy of
transition. Why is this difference so great?
I am attaching my mdp file for annealing:
title = Argon Aneling
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 2 * 50000000 = 100ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxtcout = 500
xtc-precision = 1000
; Bond parameters
continuation = yes
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
rlist= 2.724
ns_type = grid ; search neighboring grid cells
nstlist = 40 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 2.624 ; short-range electrostatic cutoff (in nm)
vdw-modifier = Potential-switch
rvdw-switch= 2.55375 ;
rvdw = 2.624 ; short-range van der Waals cutoff (in nm)
; Electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is off
tcoupl = V-rescale
tc-grps = Ar ;modified Berendsen thermostat V-rescale
tau_t = 0.01 ; time constant, in ps 0.1
ref_t = 100
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in anneling
Parrinello-Rahman
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 10 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
nstpcouple = 20 ; 5
compressibility = 7.9e-5 ; isothermal compressibility of
argon, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = single
; Number of time points to use for specifying annealing in each group
annealing_npoints = 2
; List of times at the annealing points for each group
annealing_time = 0 100000
; Temp. at each annealing point, for each group.
annealing_temp = 100 25
; Velocity generation
gen_vel = no ; Velocities are read from the trajectory
Thank you very much
Happy New Year
Bach . Romulo L. Cruz Simbron
Laboratorio de Investigacion Fisicoquimica
Universidad Nacional de Ingenieria
Av. Tupac Amaru 210 Rimac- Lima
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