[gmx-users] pressure_coupling
tarak karmakar
tarak20489 at gmail.com
Wed Nov 21 15:03:17 CET 2012
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.
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
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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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--
Tarak
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