[gmx-users] Pressure Coupling Problem
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 9 15:36:58 CEST 2009
Joe Joe wrote:
> So I got my small water box (800 waters) to behave stably with pressure
> coupling after more minimization but I still can't get my large system
> to work with pressure coupling. I tried minimizing but I can never get
> the Fmax to be less 10^2, which is pretty normal for protein/water
> simulations of large proteins, at least from my experience. I have
> since run 400 ps NVT as the system (425K atoms) is quite stable. The
> <P.E.> is 2E-05. Since I am using 4fs time steps gromacs won't let me
> use a tau_p less than .4. Not sure what else to do except run NVT, which
> is what I was going to do after I got the density equilibrated. BTW, I
> am using octahedral PBC, but that should not make a difference with
> respect to P coupling, should it? Below is my whole mdp file. As a
> reminder my density in the system goes from 1.0 - .1 in 10 ps with
> Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the amount
> of time it takes for my system to expand increases but it still expands.
>
This seems truly bizarre. How are you measuring the density (g_density,
g_energy, etc)? What are your box dimensions doing? To get that kind of sudden
change in density, your box dimensions would have to expand astronomically?
It's also curious that your 425K-atom system only has a PE on the order of 10^5;
my systems with 100K-200K have around 10^6 - 10^7; are you sure the minimization
is reasonable, and you are not simply seeing the effects of the classic "blowing
up" problem? What does your trajectory show? If you have multiple proteins or
other large species present, does minimization of each component individually
prior to system assembly help?
-Justin
> ;
> ; File 'mdout.mdp' was generated
> ; By user: relly (508)
> ; On host: master.simprota.com <http://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
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 0
> ld-seed = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 10
> emstep = 0.01
> ; Max number of iterations in relax_shells
> niter = 20
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; TEST PARTICLE INSERTION OPTIONS
> rtpi = 0.05
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 12500
> 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 = Protein SOL
>
> ; 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 = .8
> 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
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = No
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
> sa_surface_tension = 2.092
>
> ; 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 = 1.0
> ref_t = 298.0
> ; Pressure coupling
> Pcoupl = No
> 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
>
> ; OPTIONS FOR QMMM calculations
> QMMM = no
> ; Groups treated Quantum Mechanically
> QMMM-grps =
> ; QM method
> QMmethod =
> ; QMMM scheme
> QMMMscheme = normal
> ; QM basisset
> QMbasis =
> ; QM charge
> QMcharge =
> ; QM multiplicity
> QMmult =
> ; Surface Hopping
> SH =
> ; CAS space options
> CASorbitals =
> CASelectrons =
> SAon =
> SAoff =
> SAsteps =
> ; Scale factor for MM charges
> MMChargeScaleFactor = 1
> ; Optimization of QM subsystem
> bOPT =
> bTS =
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing =
> ; Number of time points to use for specifying annealing in each group
> annealing_npoints =
> ; List of times at the annealing points for each group
> annealing_time =
> ; Temp. at each annealing point, for each group.
> annealing_temp =
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 298.0
> gen-seed = 173529
>
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> ; Type of constraint algorithm
> constraint-algorithm = lincs
> ; Do not constrain the start configuration
> continuation = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 6
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 2
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl =
>
> ; WALLS
> ; Number of walls, type, atom types, densities and box-z scale factor
> for Ewald
> nwall = 0
> wall_type = 9-3
> wall_r_linpot = -1
> wall_atomtype =
>
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = no
>
> ; NMR refinement stuff
> ; Distance restraints type: No, Simple or Ensemble
> disre = No
> ; Force weighting of pairs in one distance restraint: Conservative or Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
> ; Orientation restraints: No or Yes
> orire = no
> ; Orientation restraints force constant and tau for time averaging
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> ; Output frequency for trace(SD) and S to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No or Yes
> dihre = no
> dihre-fc = 1000
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> sc-alpha = 0
> sc-power = 0
> sc-sigma = 0.3
> couple-moltype =
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw-q
> couple-intramol = no
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
> deform =
>
> ; Electric fields
> ; Format is number of terms (int) and for all terms an amplitude (real)
> ; and a phase angle (real)
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z =
> E-zt =
>
>
>
> On Wed, Apr 8, 2009 at 1:00 PM, Joe Joe <ilchorny at gmail.com
> <mailto:ilchorny at gmail.com>> wrote:
>
>
>
> On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz <roland at utk.edu
> <mailto:roland at utk.edu>> wrote:
>
>
>
> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <ilchorny at gmail.com
> <mailto:ilchorny at gmail.com>> wrote:
>
> HI Chris,
>
> On Tue, Apr 7, 2009 at 9:31 PM, <chris.neale at utoronto.ca
> <mailto: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
> <http://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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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