AW: [gmx-users] pressure_coupling
Florian Dommert
dommert at icp.uni-stuttgart.de
Wed Nov 21 15:38:31 CET 2012
-------
Florian Dommert
Dipl. Phys.
Institut für Computerphysik
Universität Stuttgart
Allmandring 3
D-70569 Stuttgart
Tel.: 0711-68563613
Fax: 0711-68563658
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von tarak karmakar
> Gesendet: Mittwoch, 21. November 2012 15:03
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
>
> Thanks for the information Flo.
> Before doing NPT I have already equilibrated my system by heating it from
0K to
> 300K in 300 ps, then the pressure has reached to 1 bar. Now while doing
NPT I'm
> getting the excess pressure.
> Is there any problem with the coupling constant ? I am checking it by
taking
> different tau_p values. Let's see.
>
I don't think that playing around with the coupling constant will help you.
You can set it to extreme values, but you won't see any difference. The
coupling constant determines, how fast the system pressure should relax to
the reference pressure. I would see a better possibility to play around by
simulating for a longer time. Then observing the variation of the pressure
in time, the size of the fluctuation and the excess pressure. Perhaps
something will change, but I don't think so. I play around with the coupling
constants but observed no change.
Maybe, but this is really speculation, there is a problem with the
combination of constraints and MTTK. Please check the archives of the user
and developer list to obtain more information.
/Flo
>
> On Wed, Nov 21, 2012 at 1:16 AM, Florian Dommert <dommert at icp.uni-
> stuttgart.de> wrote:
> >> -----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
> >> >>
> >> >> ========================================
> >> >> --
> >> >> gmx-users mailing list gmx-users at gromacs.org
> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> * Please search the archive at
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> >> >> www interface or send it to gmx-users-request at gromacs.org.
> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> >
> >> >
> >> > -
> >> >
> >>
> >> --
> >> ========================================
> >>
> >> 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
> >>
> >> ========================================
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > interface or
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> >
> > --
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>
>
> --
> Tarak
> --
> gmx-users mailing list gmx-users at gromacs.org
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