AW: [gmx-users] pressure_coupling
Florian Dommert
dommert at icp.uni-stuttgart.de
Tue Nov 20 20:46:27 CET 2012
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Justin Lemkul
> Gesendet: Dienstag, 20. November 2012 18:33
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
>
>
>
> On 11/20/12 12:29 PM, tarak karmakar wrote:
> > Thanks Justin for the quick reply.
> > Is there any problem with the algorithms ??
> >
> > I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
> > has been used to constrains the H-covalent bonds.
> > tau_t = 1 ps
> > tau_P = 1 ps
> > I got the mean pressure at ~130 bar.
> >
> > Previously with the same initial coordinates I have used Leap-Frog,
> > NH, Parinello-Rehman with LINCS to constrain H-covalent bonds.
> > tau_t was 0.1 ps
> > and tau P was 2 ps.
> > The I have seen the pressure fluctuating around 1 bar( as expected) So
> > can you please inform me from where this problem is coming -
> > algorithms and/ tau_t and tau_P parameters ?
> >
>
> I have no personal experience with the md-vv/MTTK combination. The way to
> test if there is a bug or something is to take an equilibrated system (as
suggested
> before) and continue it with the desired parameters. If they deviate or
> incorrectly report pressure, then there's probably a bug. I'm not ready
to
> conclude that until it is tested though.
>
> -Justin
>
I once tried to use the same combination of T and P coupling and MD-vv for a
system, which could be simulated with PR at 1bar without problems. But I
also observed this large pressure. Somehow I have in mind, that there was
recently a thread about MTTK coupling on the list with the conclusion that
MTTK is so far not stable, but please check the archives to assure this.
/Flo
> > On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >> On 11/20/12 11:26 AM, tarak karmakar wrote:
> >>>
> >>> Dear All,
> >>>
> >>> I want to keep the pressure at 1.0 bar during the NPT simulation.
> >>> But it is fluctuating around 130 bar. So can anyone please inform me
> >>> whether I have missed any keyword in my .mdp file OR is it because
> >>> of the tau_p which I set 1s 1.0 ps.
> >>
> >>
> >> Equilibrate with a weak coupling method (Berendsen) and then proceed
> >> using better algorithms.
> >>
> >> -Justin
> >>
> >>
> >>> Thanks
> >>>
> >>> The .mdp file is given below
> >>>
> >>>
> >>>
> >>> ; 7.3.3 Run Control
> >>> integrator = md-vv ; md integrator
> >>> tinit = 0 ; [ps] starting time
for
> >>> run
> >>> dt = 0.001 ; [ps] time step for
> >>> integration
> >>> nsteps = 15000000 ; maximum number of
> >>> steps to integrate, 0.001 * 15,00,000 = 15 ns
> >>> nstcomm = 1 ; [steps] frequency of
> >>> mass motion removal
> >>> comm_grps = Protein Non-Protein ; group(s) for center
> >>> of mass motion removal
> >>>
> >>> ; 7.3.8 Output Control
> >>> nstxout = 10000 ; [steps] freq to write
> >>> coordinates to trajectory
> >>> nstvout = 10000 ; [steps] freq to write
> >>> velocities to trajectory
> >>> nstfout = 10000 ; [steps] freq to write forces
> >>> to trajectory
> >>> nstlog = 1000 ; [steps] freq to write
> >>> energies to log file
> >>> nstenergy = 1000 ; [steps] freq to write
> >>> energies to energy file
> >>> nstxtcout = 1000 ; [steps] freq to write
> >>> coordinates to xtc trajectory
> >>> xtc_precision = 1000 ; [real] precision to write
> >>> xtc trajectory
> >>> xtc_grps = System ; group(s) to write to xtc
> >>> trajectory
> >>> energygrps = System ; group(s) to write to energy
file
> >>>
> >>> ; 7.3.9 Neighbor Searching
> >>> nstlist = 1 ; [steps] freq to update
neighbor
> >>> list
> >>> ns_type = grid ; method of updating neighbor
list
> >>> pbc = xyz ; periodic boundary conditions
> >>> in all directions
> >>> rlist = 1.2 ; [nm] cut-off distance for
> >>> the short-range neighbor list
> >>>
> >>> nsttcouple = 1
> >>> nstpcouple = 1
> >>>
> >>> ; 7.3.10 Electrostatics
> >>> coulombtype = PME ; Particle-Mesh Ewald
> >>> electrostatics
> >>> rcoulomb = 1.2 ; [nm] distance for Coulomb
> >>> cut-off
> >>>
> >>> ; 7.3.11 VdW
> >>> vdwtype = cut-off ; twin-range cut-off with
> >>> rlist where rvdw >= rlist
> >>> rvdw = 1.2 ; [nm] distance for LJ cut-off
> >>> DispCorr = EnerPres ; apply long range dispersion
> >>> corrections for energy
> >>>
> >>> ; 7.3.13 Ewald
> >>> fourierspacing = 0.12 ; [nm] grid spacing for FFT
> >>> grid when using PME
> >>> pme_order = 4 ; interpolation order for PME,
4 =
> >>> cubic
> >>> ewald_rtol = 1e-5 ; relative strength of
> >>> Ewald-shifted potential at rcoulomb
> >>>
> >>> ; 7.3.14 Temperature Coupling
> >>> tcoupl = Nose-Hoover ; Nose-Hoover
> >>> temperature coupling
> >>> tc_grps = Protein Non-Protein ; groups to
> >>> couple seperately to temperature bath
> >>> tau_t = 1.0 1.0 ; [ps] time
> >>> constant for coupling
> >>> ref_t = 300 300 ; [K]
> >>> reference temperature for coupling
> >>>
> >>> ; 7.3.15 Pressure Coupling
> >>> pcoupl = MTTK ; pressure coupling
> >>> where box vectors are variable
> >>> pcoupltype = isotropic ; pressure coupling in
> >>> x-y-z directions
> >>> tau_p = 1.0 ; [ps] time constant
> >>> for coupling
> >>> compressibility = 4.5e-5 ; [bar^-1]
compressibility
> >>> ref_p = 1.0 ; [bar] reference
> >>> pressure for coupling
> >>>
> >>> ; 7.3.17 Velocity Generation
> >>> gen_vel = no ; velocity generation turned
off
> >>>
> >>> ; 7.3.18 Bonds
> >>> constraints = h-bonds
> >>> constraint_algorithm = SHAKE ; SHAKE Constraint Solver
> >>> shake_tol = 1.0e-5
> >>>
> >>>
> >>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >> --
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> >
> >
> >
> > -
> >
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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