[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84

[Shuangxing Dai]

Well, the final average pressure is not correct:

* **<======  ###############  ==>*
* **<====  A V E R A G E S  ====>*
* **<==  ###############  ======>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
*
*    1.60633e+06   -5.69243e+06   -3.45003e+06   -7.53612e+06    1.80719e+04
*
*   Total Energy    Temperature Pressure (bar)*
*   -7.51805e+06    3.62347e+02    1.11758e+04*
*
*
*
*
*   Pressure (bar)*
*    1.21051e+04   -2.94017e-01    1.30456e+00*
*   -2.94017e-01    9.03597e+03   -8.10850e-01*
*    1.30456e+00   -8.10850e-01    1.23863e+04*
*
*
*
*
* **<======  ###############################  ==>*
* **<====  R M S - F L U C T U A T I O N S  ====>*
* **<==  ###############################  ======>*
*
*
*   Energies (kJ/mol)*
*  Buck.ham (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
*
*    3.92376e+05    4.00326e+05    4.71365e+01    3.02978e+04    2.35039e+03
*
*   Total Energy    Temperature Pressure (bar)*
*    3.01091e+04    4.71259e+01    1.71117e+05*
*
*
*
*
*   Pressure (bar)*
*    1.82323e+05    4.91513e+02    3.07107e+02*
*    4.91513e+02    2.02402e+05    3.13857e+02*
*    3.07107e+02    3.13857e+02    1.30179e+05*
*
*
*Also the fluctuation is very large. I think 200ps is long enough. But still
I cannot find the equilibrium.*
*I do not know whether the parameters are wrong or I ran the anisotropic
pressure coupling wrong. Is *Parrinello-Rahman pressure coupling sensitive
to the initial pressure? I mean if the initial pressure ( in order of GPa),
object pressure is 1 bar ( 1e5 Pa).
*
*
Thanks,
Shuangxing Dai


On Mon, Jun 14, 2010 at 8:50 PM, <gmx-users-request at gromacs.org> wrote:
>
>
> Message: 3
> Date: Mon, 14 Jun 2010 19:18:14 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] anisotropic pressure coupling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4C16B8B6.4010005 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> 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
> >
>
> --
> ========================================
>
> 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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