[gmx-users] Gromacs 4.0.2 vs. 4.0.3

Thu Apr 2 14:47:30 CEST 2009

Hi,

no, with Berendsen results appear similar between 4.0.2 and 4.0.4. I  
certainly agree about using 4.0.4, however, we did a couple of  
simulations with 4.0.2, which we probably have to repeat now:-(

Best
Rainer

On Apr 2, 2009, at 2:34 PM, Berk Hess wrote:

> 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/
> > ___________________________________________________________
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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>
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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/
___________________________________________________________