[gmx-users] pressure_coupling
tarak karmakar
tarak20489 at gmail.com
Tue Nov 20 18:29:38 CET 2012
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 ?
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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