[gmx-users] g_energy problem with 4.5.1 and 4.5.2

[Michael Brunsteiner]

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