AW: [gmx-users] pressure_coupling
Florian Dommert
dommert at icp.uni-stuttgart.de
Thu Nov 22 10:27:18 CET 2012
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von tarak karmakar
> Gesendet: Donnerstag, 22. November 2012 10:15
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
>
> U r right FLorian
> I have also tried playing around the tau_p but in vain.
> Even in absence of any constraints, it is giving almost same result.
> Em thinking to move again to Leap-Frog, NH , PR. I see people generally
use this
> combination a lot.
> Thanks
>
> Tarak
Yes, that is right. The reason might be, that it is stable, working with
Leap-Frog and implemented in Gromacs. However actually PR does not produce
an NpT but an isoenthalpic ensemble. It also does not conform to both
pressure virial theorems (see appendix of the Nose paper cited in the
Gromacs manual). For this reason it would be very very good, if MTTK would
work in Gromacs, because it fulfills all requirements for an NpT ensemble.
On the other hand side the deviations vanish in the thermodynamic limit, so
if your system is large enough, there should be no significant difference.
/Flo
>
> On Wed, Nov 21, 2012 at 8:08 PM, Florian Dommert <dommert at icp.uni-
> stuttgart.de> wrote:
> >
> >
> > -------
> > 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
> >> >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> >> >> >> * Please don't post (un)subscribe requests to the list. Use the
> >> >> >> 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
> >> >>
> >> >> ========================================
> >> >> --
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> >> >
> >> > --
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> >>
> >>
> >> --
> >> Tarak
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
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