[gmx-users] Gromacs 4.0.2 vs. 4.0.3
Berk Hess
gmx3 at hotmail.com
Thu Apr 2 14:34:26 CEST 2009
Hi,
But with Berendsen also 4.0.2 is different from 4.0.3 and 4.0.4?
There have been no changes to the temperature coupling between 4.0.2 and 4.0.4.
Only before the 4.0.2 release there was a small fix for v-rescale:
revision 1.54.2.1
date: 2008/09/26 09:25:53; author: hess; state: Exp; lines: +2 -1
added limits for lambda with V-rescale to avoid crashes with initial zero veloci
ties
I guess it must be something else, but I have no clue what.
But since everybody should be using 4.0.4 (and certainly not 4.0.2)
we don't need to get to the bottom of this issue if 4.0.4 works correctly.
Berk
> From: rainer at bioinformatik.uni-saarland.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gromacs 4.0.2 vs. 4.0.3
> Date: Thu, 2 Apr 2009 12:42:45 +0200
>
> 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/
> ___________________________________________________________
>
>
>
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