[gmx-users] TPI Results differ in v4.5.7 and v4.6.1

Niels Müller uni at nielsm.de
Mon Jun 24 16:40:04 CEST 2013


Hi João,

Indeed your instinct seems to be good! When switching the Coulomb-Type to Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5.
Apparently its an issue with the PME sum. We will investigate further.


Am 24.06.2013 um 14:42 schrieb João M. Damas <jmdamas at itqb.unl.pt>:

> Niels,
> 
> This is very interesting. At our group, a colleague of mine and I have also
> identified differences in the TPI integrator between 4.0.X and 4.5.X, but
> we still haven't had the time to report it properly, since we are using a
> slightly modified version of the TPI algorithm.
> 
> Instinctively, we were attributing it to some different behaviours in the
> RF that are observed between those versions. We also know that the TPI
> algorithm began allowing PME treatment from 4.5.X onwards, so maybe there
> are some differences going on the electrostatics level? But, IIRC, no
> modifications to the TPI code were on the release notes from 4.5.X to
> 4.6.X...
> 
> We'll try to find some time to report our findings as soon as possible.
> Maybe they are related.
> 
> Best,
> João
> 
> 
> On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller <uni at nielsm.de> wrote:
> 
>> Hi GMX Users,
>> 
>> We are computing the chemical potential of different gas molecules in a
>> polymer melt with the tpi integrator.
>> The computations are done for CO2 and CH4.
>> The previous computations were done with v4.5.5 or 4.5.7 and gave equal
>> results.
>> 
>> I recently switched to gromacs version 4.6.1, and the chemical potential
>> computed by this version is shifted by a nearly constant factor, which is
>> different for the two gas molecules.
>> We are perplexed what causes this shift. Was there any change in the new
>> version that affects the tpi integration? I will provide the mdp file we
>> used below.
>> 
>> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT
>> simulation with 'mdrun -rerun'.
>> 
>> Best regards,
>> Niels.
>> 
>> #########################
>> The mdp file:
>> #########################
>> 
>> ; VARIOUS PREPROCESSING OPTIONS
>> cpp                      = cpp
>> include                =
>> define                  =
>> 
>> ; RUN CONTROL PARAMETERS
>> integrator               = tpi
>> ; Start time and timestep in ps
>> tinit                    = 0
>> dt                       = 0.001
>> nsteps                   = 1000000
>> ; 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                  = 0.5
>> ld-seed                  = 1993
>> 
>> ; ENERGY MINIMIZATION OPTIONS
>> ; Force tolerance and initial step-size
>> emtol                    = 100
>> 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                  = 100
>> nstvout                  = 0
>> nstfout                  = 0
>> ; Checkpointing helps you continue after crashes
>> nstcheckpoint            = 100
>> ; Output frequency for energies to log file and energy file
>> nstlog                   = 100
>> nstenergy                = 100
>> ; Output frequency and precision for xtc file
>> nstxtcout                = 0
>> 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               =
>> 
>> ; 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                    = 0.9
>> domain-decomposition     = no
>> 
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype              = pme
>> rcoulomb-switch          = 0
>> rcoulomb                 = 0.9
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>> epsilon-r                = 1
>> ; Method for doing Van der Waals
>> vdw-type                 = Cut-off
>> ; cut-off lengths
>> rvdw-switch              = 0
>> rvdw                     = 0.9
>> ; 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                = 4
>> ewald_rtol               = 1e-05
>> 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                   = V-rescale
>> ; Groups to couple separately
>> tc-grps                  = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t                    = 0.1
>> ref_t                    = 318
>> ; Pressure coupling
>> Pcoupl                 = Parrinello-Rahman
>> Pcoupltype               = isotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>> tau_p                    = 5.0
>> 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                = 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                  = yes
>> gen_temp                 = 400
>> gen_seed                 = 1993
>> 
>> ; OPTIONS FOR BONDS
>> ;constraints              = none
>> 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
>> 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
>> 
>> ; Free energy control stuff
>> free-energy              = no
>> init-lambda              = 0
>> delta-lambda             = 0
>> sc-alpha                 = 0
>> sc-sigma                 = 0.3
>> 
>> ; Non-equilibrium MD stuff
>> acc-grps                 =
>> accelerate               =
>> freezegrps               =
>> freezedim                =
>> cos-acceleration         = 0
>> 
>> 
>> --
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> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> --
> gmx-users mailing list    gmx-users at gromacs.org
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