[gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:
> Reply inline...
> 
> On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     <http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman>

Bugzilla entry 14 is ancient, and has long since been resolved:

http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues

> 
>         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
> 

Do you run any equilibration prior to applying these parameters?  Both N-H and 
P-R allow for wide fluctuations in temperature and pressure, respectively, which 
are exacerbated by systems that are not sufficiently equilibrated.  Hence it 
could take a very long time if you do not equilibrate well using, i.e. a weak 
coupling scheme first.

-Justin

> 
> 
>  
> 
>     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 <http://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.

-- 
========================================

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

========================================