[gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

Reply inline...

On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I have a system of 3600 LJ particles in a plane (using freeze-dimension
>> option in z). I am running npt runs using Semi-isotropic pressure coupling
>> with Parrinello-Rahman barostat. I have a few concerns:
>>
>> 1) On the gromacs website, a webpage mentions that this type of pressure
>> coupling may not be accurate
>>
>>
> Please provide a link when making this kind of statement.
>
> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman
>
>  2) It takes a really long time for the system to reach the reference
>> pressure  > 500ns. Particularly the Pxx, Pyy terms are very different and
>> take an extremely long time to converge to a common value.
>>
>>  integrator               = md
> dt                       = 0.001
> nsteps                   = 50000000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0  ; No output, except for last frame
> (coordinates)
> nstvout                  = 0    ; No output, except for last frame
> (velocities)
> nstfout                  = 0    ; No output, except for last frame (forces)
> nstlog                   = 1000000   ; Write every nth step to the log
> nstenergy                = 1000000     ; Write energies at every n step
> nstxtcout                = 1000000     ; Do not write a compressed tr
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 10
> ns-type                  = Grid
> pbc                      = xyz
> rlist                    = 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = Cut-off
> rcoulomb                 = 1.1225
> vdw-type                 = User
> rvdw                     = 1.1225
> table-extension          = 0
>
> ; Temperature coupling
> tcoupl                   = nose-hoover
> tc-grps                  = ARAR
> tau_t                    = 0.1
> ref_t                    = 120.2717
>
> ; Pressure coupling
> pcoupl                   = Parrinello-Rahman
> pcoupltype               = semiisotropic
> tau-p                    = 1.0  1.0
> compressibility          = 1e-5  0   ;Dont know
> ref-p                    = 69 0
>
>
> ;Generate velocities for startup run
> gen_vel                  =no
> gen_temp                 =120.2717
> gen_seed                 =-1
>
> ;Non equilibrium MD steps
freezegrps              =ARAR
freezedim               =N N Y

;Constraints
constraints             = all-bonds
constraint_algorithm    = Lincs
lincs_order             = 4
lincs_iter              = 1
lincs_warnangle         = 90
;unconstrained_start    = no
;shake_tol              = 0.0001





> What was your equilibration protocol?  What are your .mdp settings?
>
> -Justin
>
>
>  Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> ========================================
>
> 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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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