[gmx-users] pressure_coupling
tarak karmakar
tarak20489 at gmail.com
Thu Nov 22 10:15:13 CET 2012
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
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
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>> >> >> * 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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>> >
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>>
>>
>> --
>> Tarak
>> --
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