[gmx-users] anisotropic pressure coupling

[Justin A. Lemkul]

Shuangxing Dai wrote:
> Hi all:
>     I was using Parrinello-Rahman for pressure coupling and here is the 
> mdp file:
> 
> ; RUN CONTROL PARAMETERS =
> integrator               = sd
> ; start time and timestep in ps =
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 200000
> ; number of steps for center of mass motion removal =
> nstcomm                  = 100
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 50
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> 
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl                   = Parrinello-Rahman
> pcoupltype               = anisotropic
> tau_p                    = 1
> compressibility          = 2.1645e-09  2.1645e-09 2.7322e-09 0 0 0
> ref_p                    = 1 1 1 0 0 0
> ;OPTIONS FOR TEMPERATURE COUPLING
> tc_grps                  = system
> tau_t                    = 0.1
> ref_t                    = 300
> ; OPTIONS FOR BONDS     =
> constraints              = hbonds
> ; Type of constraint algorithm =
> constraint-algorithm     = Lincs
> ; Do not constrain the start configuration =
> unconstrained-start      = no
> ; Relative tolerance of shake =
> shake-tol                = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs-order              = 12
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs-warnangle          = 30
> ; Periodic boundary conditions: xyz, no, xy
> pbc                      = xyz
> periodic_molecules       = no
> ; nblist cut-off        
> rlist                    = 1
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> rcoulomb                 = 1
> ; Method for doing Van der Waals
> vdw-type                 = Cut-off
> ; cut-off lengths       
> rvdw                     = 1
> 
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-4
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
> 
>  It seems that the temperature coupling is fast and fluctuation is less 
> that 1%. But the pressure coupling fails. The pressure fluctuates from 
> +1e3 bar to -1e3 bar. Anyone can help?
> 

I don't call that failure.  Depending on the size of your system, you can 
probably expect very wide fluctuations in the pressure.  Is the average correct?

http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin

> 
> Thanks,
> Shuangxing Dai
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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