[gmx-users] Pressure Coupling Problem
Joe Joe
ilchorny at gmail.com
Wed Apr 8 22:00:42 CEST 2009
On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz <roland at utk.edu> wrote:
>
>
> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <ilchorny at gmail.com> wrote:
>
>> HI Chris,
>>
>> On Tue, Apr 7, 2009 at 9:31 PM, <chris.neale at utoronto.ca> wrote:
>>
>>> Hi Ilya,
>>>
>>> First thing that comes to mind is that it is strange to couple a
>>> coulombic switching function with PME. While this could possibly be done
>>> correctly, I doubt that it is in fact done in the way that you expect (i.e.
>>> correctly) in gromacs. In fact, I think that grompp/mdrun should probably
>>> throw an error here -- unless it is actually handled in the proper way, and
>>> a developer could help you here to figure out if you are indeed getting what
>>> you desire.
>>>
>>> coulombtype = PME
>>> rcoulomb-switch = .9
>>> rcoulomb = 1.0
>>
>>
>> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
>> of PME but I will give it a try.
>>
>
> It is indeed supported and does work correctly. But you have to set
> coulombtype PME-Switch. mdp options says:
> "This is mainly useful constant energy simulations. For constant
> temperature simulations the advantage of improved energy conservation is
> usually outweighed by the small loss in accuracy of the electrostatics. "
>
> Roland
>
Yes, my point was that when electrostatics = PME then Gromacs ignores the
rcoulomb-switch parameter.
>
>
>
>>
>>>
>>> Chris
>>>
>>> -- original message --
>>>
>>> Hi
>>> I am having some pressure coupling issues. I have a fairly large
>>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
>>> run NVE it conserves energy with appropriate parameter settings. If I run
>>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
>>> Rahman), the system just continuously expands. My parameters are as
>>> follows.
>>> Any ideas?
>>>
>>> Best,
>>>
>>> Ilya
>>>
>>> ;
>>> ; File 'mdout.mdp' was generated
>>> ; By user: relly (508)
>>> ; On host: master.simprota.com
>>> ; At date: Fri Mar 6 20:17:33 2009
>>> ;
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> ; Preprocessor information: use cpp syntax.
>>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>>> include =
>>> ; e.g.: -DI_Want_Cookies -DMe_Too
>>> define =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator = md
>>> ; Start time and timestep in ps
>>> tinit = 0
>>> dt = 0.004
>>> ;nsteps = 250000
>>> nsteps = 2500000
>>> ; For exact run continuation or redoing part of a run
>>> ; Part index is updated automatically on checkpointing (keeps files
>>> separate)
>>> simulation_part = 1
>>> init_step = 0
>>> ; mode for center of mass motion removal
>>> comm_mode = linear
>>> ; number of steps for center of mass motion removal
>>> nstcomm = 1
>>> ; group(s) for center of mass motion removal
>>> comm_grps = system
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>> nstxout = 0
>>> nstvout = 0
>>> nstfout = 0
>>>
>>> ; Output frequency for energies to log file and energy file
>>> nstlog = 10
>>> nstenergy = 10
>>> ; Output frequency and precision for xtc file
>>> nstxtcout = 250
>>> xtc-precision = 1000
>>> ; This selects the subset of atoms for the xtc file. You can
>>> ; select multiple groups. By default all atoms will be written.
>>> xtc-grps = protein
>>> ; Selection of energy groups
>>> energygrps =
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS
>>> ; nblist update frequency
>>> nstlist = 5
>>> ; ns algorithm (simple or grid)
>>> ns_type = grid
>>> ; Periodic boundary conditions: xyz, no, xy
>>> pbc = xyz
>>> periodic_molecules = no
>>> ; nblist cut-off
>>> rlist = 1.0
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>> ; Method for doing electrostatics
>>> coulombtype = PME
>>> rcoulomb-switch = .9
>>> rcoulomb = 1.0
>>> ; Relative dielectric constant for the medium and the reaction field
>>> epsilon-r = 80
>>> epsilon_rf = 1
>>> ; Method for doing Van der Waals
>>> vdw-type = Switch
>>> ; cut-off lengths
>>> rvdw-switch = .9
>>> rvdw = 1.0
>>> ; Apply long range dispersion corrections for Energy and Pressure
>>> DispCorr = EnerPres
>>> ; Extension of the potential lookup tables beyond the cut-off
>>> table-extension = 1
>>> ; Seperate tables between energy group pairs
>>> energygrp_table =
>>> ; 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 = 4
>>> ewald_rtol = 1.e-05
>>> ewald_geometry = 3d
>>> epsilon_surface = 0
>>> optimize_fft = no
>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>>> ; Temperature coupling
>>> Tcoupl = V-rescale
>>> ; Groups to couple separately
>>> tc-grps = System
>>> ; Time constant (ps) and reference temperature (K)
>>> tau_t = 0.1
>>> ref_t = 298.0
>>> ; Pressure coupling
>>> Pcoupl = Berendsen
>>> Pcoupltype = Isotropic
>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>>> tau_p = 10
>>> compressibility = 4.5e-5
>>> ref_p = 1.01325
>>> ; Scaling of reference coordinates, No, All or COM
>>> refcoord_scaling = No
>>> ; Random seed for Andersen thermostat
>>> andersen_seed = 815131
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>>
>>
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>
>
>
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> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
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