[gmx-users] Energy conservation in NVE simulations
张正财
zhangzhengc at mail.iggcas.ac.cn
Wed Nov 4 16:17:34 CET 2015
Dear Mark
Thanks for your reply. I used gromacs-4.5.6, so the cutoff scheme is Group. I really carefully read the manual and
I can simualte CH4/Water sytstem with goog energy conservation with my mdp file. I used shake to restrict the bond and angle in the propane molecule. Which parameter do you think affect the energy conservation in my propane/CH4/Water system?
all the best,
Zhengcai
> Hi,
>
> We need to know things like which GROMACS version, what cutoff scheme
> you're using, and whether you've thought about the comments in the manual
> about constraint settings and conservation. SHAKE + all-angles + a given
> timestep + a given convergence tolerance can't magically conserve energy.
> Whether this is the problem remains to be seen.
>
> Mark
>
> On Wed, Nov 4, 2015 at 2:57 PM ??? <zhangzhengc at mail.iggcas.ac.cn> wrote:
>
> > Dear All,
> > I am having difficulties getting gromacs to conserve energy . I
> > searched the maillist, I found the same question asked 5 years ago, but
> > there is no good answers.
> > I want to simulate Methane-Propane-water system (box size 5*5*10
> > nm) in the NVE ensemble. However, the total energy cannot be conservated,
> > the attachment is my mdp file. Using the same mdp file, I can keep total
> > energy constant during CH4-Water system. I have tested the timestep, It
> > makes no strong influence on energy drift between 1 to 2 fs. Could anyone
> > give me some advice?
> > /**********************************************************/
> > ; RUN CONTROL PARAMETERS
> > integrator = md
> > ; Start time and timestep in ps
> > tinit = 0
> > dt = 0.002
> > nsteps = 100000
> > ; 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-fric = 0
> > ld-seed = 24652
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > ; Force tolerance and initial step-size
> > emtol = 100
> > emstep = 0.001
> > ; 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 = 1000000
> > nstvout = 1000000
> > nstfout = 1000000
> > ; Checkpointing helps you continue after crashes
> > nstcheckpoint = 1000
> > ; Output frequency for energies to log file and energy file
> > nstlog = 5000
> > nstcalcenergy = 5
> > nstenergy = 5000
> > ; Output frequency and precision for xtc file
> > nstxtcout = 10000
> > xtc-precision = 10000
> > ; 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 =
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist = 5
> > ; 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 = 1.6
> > rlist_long = 1.65
> > domain-decomposition = no
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = PME-Switch
> > rcoulomb-switch = 1.2
> > rcoulomb = 1.4
> > ; Dielectric constant (DC) for cut-off or DC of reaction field
> > epsilon-r = 1
> > ; Method for doing Van der Waals
> > vdw-type = Shift
> > ; cut-off lengths
> > rvdw-switch = 1.2
> > rvdw = 1.3
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = EnerPres
> > ; 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 = 6
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = yes
> >
> > ; 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 = NO ; nose-hoover
> > Pcoupl = NO ; Parrinello-Rahman
> >
> >
> > ; SIMULATED ANNEALING
> > ; Type of annealing for each temperature group (no/single/periodic)
> > annealing = no
> > ; 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 = 24652
> >
> > ; OPTIONS FOR BONDS
> > constraints = all-angles
> > ; Type of constraint algorithm
> > constraint-algorithm = shake
> > ; 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
> > 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) to energy file
> > nstorireout = 100
> > ; Dihedral angle restraints: No, Simple or Ensemble
> > dihre = No
> > dihre-fc = 1000
> > dihre-tau = 0
> > ; Output frequency for dihedral values to energy file
> > nstdihreout = 100
> > /**********************************************************/
> > Sincerely yours,
> > Zhengcai,
> >
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