chetana baliga
2007-01-05 12:38:55 UTC
Dear all,
I am running md simulations on a decapeptide, using pressure coupling [npt].
My box is octahedral and box dimensions are set at peptide length plus twice
the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the
average pressure had come down to 2.6 bar, though fluctuations were quite
high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen
again to 4.6 bar. Can you please advise me on this? Also, can you please
tell me if there is any correlation between pressure average and tau_p
values?
I have attached the md parameters file and the mdout files with this mail.
Thanks,
Chetana.
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title = MDP file for Full MD
cpp = /lib/cpp
integrator = MD
tinit = 0
dt = 0.002
nstcomm = 1
nsteps = 500000 ; 1 ns (run control)
nstxout = 10000
nstvout = 10000
nstxtcout = 250
nstenergy = 250
energygrps = Protein SOL ;(output control)
nstlist = 10
ns_type = grid
rlist = 1.1 ;(neighbor searching)
coulombtype = PME
;rcoulomb_switch = 1.0
rcoulomb = 1.0
vdwtype = shift
rvdw_switch = 0.9
rvdw = 1.0
fourierspacing = 0.12 ;(nm)
ewald_rtol = 1e-5
pme_order = 4 ;(electrostatics and VDW)
tcoupl = berendsen
tc_grps = Protein SOL NA+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300;(Temperature coupling)
; pressure coupling is on
pcoupl = berendsen
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
constraints = all-bonds
constraint_algorithm = lincs
-------------- next part --------------
; File 'mdout.mdp' was generated
; By user: chetana (501)
; On host: alanine
; At date: Mon Jan 1 12:28:06 2007
;
; VARIOUS PREPROCESSING OPTIONS
title = MDP file for Full MD
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = MD
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 500000
; For exact run continuation or redoing part of a run
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 =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-temp = 300
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 (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10000
nstvout = 10000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 250
; 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 =
; Selection of energy groups
energygrps = Protein SOL
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdwtype = shift
; cut-off lengths
rvdw_switch = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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 = 1e-5
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = 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
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately
tc_grps = Protein SOL NA+
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Pressure coupling
pcoupl = berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; 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 = no
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint_algorithm = lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; 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 = 1
; 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 =
; 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
I am running md simulations on a decapeptide, using pressure coupling [npt].
My box is octahedral and box dimensions are set at peptide length plus twice
the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the
average pressure had come down to 2.6 bar, though fluctuations were quite
high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen
again to 4.6 bar. Can you please advise me on this? Also, can you please
tell me if there is any correlation between pressure average and tau_p
values?
I have attached the md parameters file and the mdout files with this mail.
Thanks,
Chetana.
-------------- next part --------------
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-------------- next part --------------
title = MDP file for Full MD
cpp = /lib/cpp
integrator = MD
tinit = 0
dt = 0.002
nstcomm = 1
nsteps = 500000 ; 1 ns (run control)
nstxout = 10000
nstvout = 10000
nstxtcout = 250
nstenergy = 250
energygrps = Protein SOL ;(output control)
nstlist = 10
ns_type = grid
rlist = 1.1 ;(neighbor searching)
coulombtype = PME
;rcoulomb_switch = 1.0
rcoulomb = 1.0
vdwtype = shift
rvdw_switch = 0.9
rvdw = 1.0
fourierspacing = 0.12 ;(nm)
ewald_rtol = 1e-5
pme_order = 4 ;(electrostatics and VDW)
tcoupl = berendsen
tc_grps = Protein SOL NA+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300;(Temperature coupling)
; pressure coupling is on
pcoupl = berendsen
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
constraints = all-bonds
constraint_algorithm = lincs
-------------- next part --------------
; File 'mdout.mdp' was generated
; By user: chetana (501)
; On host: alanine
; At date: Mon Jan 1 12:28:06 2007
;
; VARIOUS PREPROCESSING OPTIONS
title = MDP file for Full MD
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = MD
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 500000
; For exact run continuation or redoing part of a run
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 =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-temp = 300
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 (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10000
nstvout = 10000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 250
; 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 =
; Selection of energy groups
energygrps = Protein SOL
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdwtype = shift
; cut-off lengths
rvdw_switch = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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 = 1e-5
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = 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
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately
tc_grps = Protein SOL NA+
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Pressure coupling
pcoupl = berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; 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 = no
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint_algorithm = lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; 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 = 1
; 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 =
; 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