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

[Mark Abraham]

Hi,

It sounds like you simply haven't reached / sampled from an equilibrated
system before collecting data.

Mark

On Mon, Jan 2, 2017 at 6:47 PM Romulo Leoncio Cruz Simbron <
romulocruzs007 at gmail.com> wrote:

> 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*
> --
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