[gmx-users] Semiisotropic Pressure coupling with PR
Sai Pooja
saipooja at gmail.com
Thu Jul 15 16:00:40 CEST 2010
Reply inline...
On Thu, Jul 15, 2010 at 9:54 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
>
I usually start with a pressure nearby. For example, I start with a system
which was equilibrated at p=71 and then run npt at p=69. Is that not
sufficient?
Pooja
> -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
>
> ========================================
> --
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--
Quaerendo Invenietis-Seek and you shall discover.
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