[gmx-users] pressure_coupling

[tarak karmakar]

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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