[gmx-users] Gromacs 4.0.2 vs. 4.0.3

[Berk Hess]

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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