[gmx-users] g_energy problem with 4.5.1 and 4.5.2

[Sander Pronk]

Hi Michael,

I've been able to reproduce both problems - I'll fix them shortly.

Sander


On 2 Nov 2010, at 10:28 , Michael Brunsteiner wrote:

> 
> Hi everybody,
> 
> I run NPT simulations (with the double precision version of mdrun) of a polymer melt
> with anisotropic pressure scaling The simulation seems to go fine, and the
> trajectories look reasonable, but there's something wrong with my g_energy output.
> 
> === With 4.5.1 I get weird values for the box dimensions.
> The g_energy output gives me something like:
> 
> Box-XX  4.7
> Box-YX  0.2
> Box-YY  5.5
> Box-ZX  0.0
> Box-ZY  0.0
> Box-ZZ  0.0
> 
> Mind you This is NOT because the box shrinks so much as both the input and
> output structures are roughly cubic with about 5 nm side-length, also if these
> values were true at least one box length would be shorter than the cut-off and
> I'd get a fatal error (which i don't). That is the values reported by g_energy are
> wrong.
> For the same system with isotropic pressure scaling there's no problem.
> 
> === If I use g_energy and mdrun versions 4.5.2 then g_energy stops working
> altogether, I get:
> 
> prompt> g_energy_d -f ener.edr -o test.xvg -s topol.tpr
> 
> "Fatal error:
> edr file with negative step number or unreasonable time (and without version number).
> If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL"
> 
> I tried both:
> prompt> export GMX_ENX_NO_FATAL=1
> or
> prompt> export GMX_ENX_NO_FATAL=1
> 
> in both cases I just get:
> 
> "File input/output error:
> Cannot read energy file header. Corrupt file?"
> 
> This I get with g_energy 4.5.2 for output from both mdrun 4.5.1 AND 4.5.2.
> 
> mdp file and sys info included below.
> 
> thanks for any feedback!
> 
> Michael
> 
> ==============================================
> 
> My system:
> 
> Linux 2.6.32-5-amd64,
> gcc 4.4.5
> GNU C Library (Debian EGLIBC 2.11.2-6+squeeze1) stable release version 2.11.2
> CPU: Intel(R) Core(TM) i7 CPU 960 @ 3.20GHz
> 
> 
> the mdp file:
> 
> integrator               = md
> nsteps                   = 250000
> dt                       = 0.002
> ;
> nstxtcout                = 0
> nstenergy                = 108
> nst_log                  = 100
> nstxout                  = 250
> nstvout                  = 0
> energygrps               = ste ca
> ;
> nstlist                  = 12
> nstype                   = grid
> pbc                      = xyz
> nstcomm                  = 100
> rlist                    = 1.2
> ;
> coulombtype              = PME
> rcoulomb                 = 1.2
> vdwtype                  = shift
> rvdw                     = 1.2
> ;
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
> fourier_nx               = 32
> fourier_ny               = 32
> fourier_nz               = 32
> ;
> constraints              = hbonds
> lincs_iter               = 4
> ;
> Tcoupl                   = nose-hoover
> tc_grps                  = System
> ref_t                    = 400.0
> tau_t                    = 0.5
> gen_vel                  = yes
> gen_temp                 = 200.0
> gen_seed                 = 222222
> ;
> Pcoupl                   = berendsen
> pcoupltype               = anisotropic
> tau_p                    = 0.5 0.5 0.5 0.5 0.5 0.5
> compressibility          = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
> ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
> 
> 
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