<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>The release notes for 4.0.3 are at:<br>http://www.gromacs.org/content/view/181/132/<br>I don't see any relevant bug fixes there and I don't recall any either.<br><br>Please update to 4.0.4, since many small bugs have been fixed.<br><br>Berk<br><br>> From: rainer@bioinformatik.uni-saarland.de<br>> To: gmx-users@gromacs.org<br>> Date: Wed, 1 Apr 2009 11:20:53 +0200<br>> CC: <br>> Subject: [gmx-users] Gromacs 4.0.2 vs. 4.0.3<br>> <br>> Hi,<br>> <br>> we performed for comparison pentadecane simulations using both the <br>> 4.0.2 version and 4.0.3, with the same mdp file (see below). Results <br>> look quite different (reproducible), for 4.0.2 the system quickly (few <br>> 100 ps) enters the crystalline phase while it stays fluid for 4.0.3 <br>> (with an increased volume/molecule). Is this due to some known bug in <br>> 4.0.2?<br>> <br>> Best<br>> Rainer<br>> <br>> <br>> integrator = md<br>> ; Start time and timestep in ps<br>> tinit = 0<br>> dt = 0.002<br>> nsteps = 5000000<br>> ; For exact run continuation or redoing part of a run<br>> ; Part index is updated automatically on checkpointing (keeps files <br>> separate)<br>> simulation_part = 1<br>> init_step = 0<br>> ; mode for center of mass motion removal<br>> comm-mode = Linear<br>> ; number of steps for center of mass motion removal<br>> nstcomm = 1<br>> ; group(s) for center of mass motion removal<br>> comm-grps = System<br>> <br>> ; LANGEVIN DYNAMICS OPTIONS<br>> ; Friction coefficient (amu/ps) and random seed<br>> bd-fric = 0<br>> ld-seed = 1993<br>> <br>> ; NEIGHBORSEARCHING PARAMETERS<br>> ; nblist update frequency<br>> nstlist = 10<br>> ; ns algorithm (simple or grid)<br>> ns_type = grid<br>> ; Periodic boundary conditions: xyz, no, xy<br>> pbc = xyz<br>> periodic_molecules = no<br>> ; nblist cut-off<br>> rlist = 1<br>> <br>> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>> ; Method for doing electrostatics<br>> coulombtype = PME<br>> rcoulomb_switch = 0<br>> rcoulomb = 1.0<br>> ; Relative dielectric constant for the medium and the reaction field<br>> epsilon_r = 1<br>> epsilon_rf = 1<br>> ; Method for doing Van der Waals<br>> vdw-type = Cut-off<br>> ; cut-off lengths<br>> rvdw_switch = 0<br>> rvdw = 1.0<br>> ; Apply long range dispersion corrections for Energy and Pressure<br>> DispCorr = EnerPres<br>> ; Extension of the potential lookup tables beyond the cut-off<br>> table-extension = 1<br>> ; Seperate tables between energy group pairs<br>> energygrp_table =<br>> ; Spacing for the PME/PPPM FFT grid<br>> fourierspacing = 0.12<br>> ; FFT grid size, when a value is 0 fourierspacing will be used<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> ; EWALD/PME/PPPM parameters<br>> pme_order = 4<br>> ewald_rtol = 1e-05<br>> ewald_geometry = 3d<br>> epsilon_surface = 1<br>> optimize_fft = no<br>> <br>> <br>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>> ; Temperature coupling<br>> Tcoupl = V-rescale<br>> ; Groups to couple separately<br>> tc_grps = System<br>> ; Time constant (ps) and reference temperature (K)<br>> tau_t = 0.1<br>> ref_t = 280<br>> ; Pressure coupling<br>> Pcoupl = Berendsen<br>> Pcoupltype = isotropic<br>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>> tau_p = 1.<br>> compressibility = 8.82e-5<br>> ref_p = 1.<br>> ; Scaling of reference coordinates, No, All or COM<br>> refcoord_scaling = No<br>> ; Random seed for Andersen thermostat<br>> andersen_seed = 815131<br>> <br>> <br>> ; GENERATE VELOCITIES FOR STARTUP RUN<br>> gen-vel = yes<br>> gen_temp = 280<br>> gen_seed = 173529<br>> <br>> ; OPTIONS FOR BONDS<br>> constraints = h-bonds<br>> ; Type of constraint algorithm<br>> constraint_algorithm = Lincs<br>> ; Do not constrain the start configuration<br>> continuation = no<br>> Shake-SOR = no<br>> shake_tol = 1e-04<br>> lincs_order = 4<br>> lincs-iter = 1<br>> incs_warnangle = 30<br>> morse = no<br>> <br>> __________________________________________________________<br>> Dr. Rainer Böckmann<br>> Theoretical & Computational Membrane Biology<br>> Center for Bioinformatics Saar<br>> Universität des Saarlandes<br>> Gebäude C7.1, EG<br>> D-66041 Saarbrücken, Germany<br>> Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180<br>> E-Mail: rainer@bioinformatik.uni-saarland.de<br>> http://www.bioinf.uni-sb.de/RB/<br>> ___________________________________________________________<br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
</html>