[gmx-users] Re: pressure_coupling
Michael Shirts
mrshirts at gmail.com
Fri Nov 23 03:34:57 CET 2012
It's in review with JCTC right now.
On Thu, Nov 22, 2012 at 2:19 PM, ABEL Stephane 175950
<Stephane.ABEL at cea.fr> wrote:
> Hello,
>
> This is a very nice and interesting work, Michael. Thank you for the efforts you made in writing this paper. I hope you will publish it.
>
> Best
>
> Stephane
>
>
> ________________________________________
>
> 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:
>>> -----Urspr?ngliche 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 f?r Computerphysik
>>> > Universit?t Stuttgart
>>> > Allmandring 3
>>> > D-70569 Stuttgart
>>> >
>>> > Tel.: 0711-68563613
>>> > Fax: 0711-68563658
>>> >
>>> >
>>> >> -----Urspr?ngliche 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:
>>> >> >> -----Urspr?ngliche 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.
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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
>>> >> >>
>>> >> >> ========================================
>>> >> >> --
>>> >> >> gmx-users mailing list gmx-users at gromacs.org
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>>> >> > interface or
>>> >> >> send it to gmx-users-request at gromacs.org.
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>>> >> >
>>> >> > --
>>> >> > gmx-users mailing list gmx-users at gromacs.org
>>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> >>
>>> >>
>>> >> --
>>> >> Tarak
>>> >> --
>>> >> gmx-users mailing list gmx-users at gromacs.org
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