[gmx-users] About the number of step in Argon Molecular Dynamic -Phase transition

[Romulo Leoncio Cruz Simbron]

P.D.:  In the first paragraph I mean the phase transition temperature

2017-01-02 12:40 GMT-05:00 Romulo Leoncio Cruz Simbron <
romulocruzs007 at gmail.com>:

> 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
>



-- 

*Rómulo Cruz Simbron*