[gmx-users] pressure_coupling
Michael Shirts
mrshirts at gmail.com
Thu Nov 22 17:03:18 CET 2012
Hi, all-
There are some issues with MTTK + constraints that are being worked
out for 4.6. The good thing is, I have developed some sensitive tests
of the correct volume distribution (see
http://arxiv.org/abs/1208.0910) and the errors in PR are very, very
small. I would recommend using md + PR for projects with code before
4.6.
On Thu, Nov 22, 2012 at 4:27 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 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
>> >> >>
>> >> >> ========================================
>> >> >> --
>> >> >> gmx-users mailing list gmx-users at gromacs.org
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>> >> >> www
>> >> > interface or
>> >> >> send it to gmx-users-request at gromacs.org.
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>> >> >
>> >> > --
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>> >>
>> >>
>> >> --
>> >> Tarak
>> >> --
>> >> gmx-users mailing list gmx-users at gromacs.org
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