[gmx-users] TPI Results differ in v4.5.7 and v4.6.1
João M. Damas
jmdamas at itqb.unl.pt
Mon Jul 1 14:29:35 CEST 2013
I have run TPI using three versions (4.0.4, 4.5.4 and 4.6.1) and three
different insertions particles: CH4 (uncharged), Cl- (negative) and Na+
(positive). All TPI were run on the same simulations of SPC water and the
three particles taken from GROMOS force-field. Reaction-field was used for
electrostatics.
https://www.dropbox.com/s/in66zx8t2mrprgt/plot_batch-1.png
As you can see, for an uncharged particle all the versions provide the same
result. The same does not happen when charged particles are inserted, which
hint on problems with the electrostatics between 4.0.4 and 4.[56].X. Like
when Niels reported for the Cut-off scheme, the reaction-field provides the
same results for 4.5.4 and 4.6.1. Is it indeed a problem with PME?
I still have not tested PME, but I think Niels' test foretells the results
I'm going to get. Niels, can you confirm this issue is only happening with
charged particles? And are you going to file an issue like Szilárd
suggested?
Best,
João
On Sat, Jun 29, 2013 at 5:21 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> 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.
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>>
>>
>> --
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>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>
--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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