[gmx-users] Gromacs 4.0.2 vs. 4.0.3

[Rainer Bockmann]

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/
___________________________________________________________