[gmx-users] pressure_coupling
Justin Lemkul
jalemkul at vt.edu
Tue Nov 20 18:32:49 CET 2012
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
> 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
>>
>> ========================================
>> --
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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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