[gmx-users] pressure_coupling

[Justin Lemkul]

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
>
>

-- 
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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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