[gmx-users] Gromacs 4.0.2 vs. 4.0.3

[Rainer Bockmann]

Hi Berk,

the difference is probably due to thermal coupling: with Berendsen  
thermostat, Gromacs versions 3.3.3 to 4.0.4 yield similar results. In  
contrast, using v-rescale, results using version 4.0.2 are  
significantly different from 4.0.3 or 4.0.4 results.

Best
Rainer


On Apr 1, 2009, at 1:10 PM, Berk Hess wrote:

> Hi,
>
> The release notes for 4.0.3 are at:
> http://www.gromacs.org/content/view/181/132/
> I don't see any relevant bug fixes there and I don't recall any  
> either.
>
> Please update to 4.0.4, since many small bugs have been fixed.
>
> Berk
>
> > From: rainer at bioinformatik.uni-saarland.de
> > To: gmx-users at gromacs.org
> > Date: Wed, 1 Apr 2009 11:20:53 +0200
> > CC:
> > Subject: [gmx-users] Gromacs 4.0.2 vs. 4.0.3
> >
> > Hi,
> >
> > we performed for comparison pentadecane simulations using both the
> > 4.0.2 version and 4.0.3, with the same mdp file (see below). Results
> > look quite different (reproducible), for 4.0.2 the system quickly  
> (few
> > 100 ps) enters the crystalline phase while it stays fluid for 4.0.3
> > (with an increased volume/molecule). Is this due to some known bug  
> in
> > 4.0.2?
> >
> > Best
> > Rainer
> >
> >
> > integrator = md
> > ; Start time and timestep in ps
> > tinit = 0
> > dt = 0.002
> > nsteps = 5000000
> > ; For exact run continuation or redoing part of a run
> > ; Part index is updated automatically on checkpointing (keeps files
> > separate)
> > simulation_part = 1
> > 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 = System
> >
> > ; LANGEVIN DYNAMICS OPTIONS
> > ; Friction coefficient (amu/ps) and random seed
> > bd-fric = 0
> > ld-seed = 1993
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist = 10
> > ; ns algorithm (simple or grid)
> > ns_type = grid
> > ; Periodic boundary conditions: xyz, no, xy
> > pbc = xyz
> > periodic_molecules = no
> > ; nblist cut-off
> > rlist = 1
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = PME
> > rcoulomb_switch = 0
> > rcoulomb = 1.0
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon_r = 1
> > epsilon_rf = 1
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off
> > ; cut-off lengths
> > rvdw_switch = 0
> > rvdw = 1.0
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = EnerPres
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension = 1
> > ; Seperate tables between energy group pairs
> > energygrp_table =
> > ; 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 = 1
> > optimize_fft = 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 = 280
> > ; Pressure coupling
> > Pcoupl = Berendsen
> > Pcoupltype = isotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau_p = 1.
> > compressibility = 8.82e-5
> > ref_p = 1.
> > ; Scaling of reference coordinates, No, All or COM
> > refcoord_scaling = No
> > ; Random seed for Andersen thermostat
> > andersen_seed = 815131
> >
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen-vel = yes
> > gen_temp = 280
> > gen_seed = 173529
> >
> > ; OPTIONS FOR BONDS
> > constraints = h-bonds
> > ; Type of constraint algorithm
> > constraint_algorithm = Lincs
> > ; Do not constrain the start configuration
> > continuation = no
> > Shake-SOR = no
> > shake_tol = 1e-04
> > lincs_order = 4
> > lincs-iter = 1
> > incs_warnangle = 30
> > morse = no
> >
> > __________________________________________________________
> > Dr. Rainer Böckmann
> > Theoretical & Computational Membrane Biology
> > Center for Bioinformatics Saar
> > Universität des Saarlandes
> > Gebäude C7.1, EG
> > D-66041 Saarbrücken, Germany
> > Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180
> > E-Mail: rainer at bioinformatik.uni-saarland.de
> > http://www.bioinf.uni-sb.de/RB/
> > ___________________________________________________________
> >
> >
> >
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__________________________________________________________
Dr. Rainer Böckmann
Theoretical & Computational Membrane Biology
Center for Bioinformatics Saar
Universität des Saarlandes
Gebäude C7.1, EG
D-66041 Saarbrücken, Germany
Phone: ++49 +681 302-64169 / 68627  FAX: ++49 +681 302-64180
E-Mail: rainer at bioinformatik.uni-saarland.de
http://www.bioinf.uni-sb.de/RB/
___________________________________________________________