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

Szilárd Páll szilard.pall at cbr.su.se
Mon Jun 24 19:00:50 CEST 2013


If you have a solid example that reproduced the problem, feel free to
file an issue on redmine.gromacs.org ASAP. Briefly documenting your
experiments and verification process on the issue report page can help
help developers in giving you faster feedback as well as with
accepting the report as a bug and fixing it (if it is one).

Cheers,
--
Szilárd


On Mon, Jun 24, 2013 at 4:40 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
>>>
>>>
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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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>
>
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