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

João M. Damas jmdamas at itqb.unl.pt
Sat Jun 29 18:21:36 CEST 2013


Niels,

Which force-field did you use? I guess an uncharged CH4 shouldn't be giving
different results for TPI when changing coulomb... Actually, coulomb is
turned off if there's no charge in the particles to insert, if I remember
the code correctly.

João


On Mon, Jun 24, 2013 at 3:40 PM, Niels Müller <uni at nielsm.de> wrote:

> 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
> >>
> >>
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> >
> > --
> > João M. Damas
> > PhD Student
> > Protein Modelling Group
> > ITQB-UNL, Oeiras, Portugal
> > Tel:+351-214469613
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613



More information about the gromacs.org_gmx-users mailing list