[gmx-users] Pressure Coupling Problem

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Apr 8 17:37:33 CEST 2009


Hi Ilya,

If you did include the entire mdp file then you have a time step of 4  
fs and no constraints (other than water). For a timestep of 2 fs, you  
should constrain all-bonds (or some would say at least h-bonds) and  
for 4 fs then you should also constrain angles involving hydrogens  
(need a new .itp file for this).

Can you try with a 1 fs timestep and see how it goes? Still, I am  
surprised that everything works out at NVT, but this is certainly  
worth the test.

Do you have other systems running fine with these mdp options in NVT?

Chris.

-- original message --

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.

>
>
> However, it is not clear to me that this should cause a system to
> "continuously expand".
>
> Still, you do not give very good information about what you mean by
> "continuously expand". Can you please provide some information on that? e.g.
> amount of time and total volume change.


My box density goes from ~1.0 to .5 in 5 ps with a compressibility of 5E-05.
  It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In both
case the slope of density(t) is negative and never levels off.


>
> 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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