[gmx-users] Pressure Coupling Problem
Joe Joe
ilchorny at gmail.com
Thu Apr 9 15:29:02 CEST 2009
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.
;
; 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
; 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> wrote:
>
>
> 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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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>> Please search the archive at http://www.gromacs.org/search before
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>
>
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