[gmx-users] program crash

[Dongsheng Zhang]

Dear GMX users,

My program crashed very soon after it started. I had done EM, and the
conformation looked fine in VMD. When I investigated what's wrong, I
outputted the coordinates, forces, velocities and log file in every
step. I set some parameters in mdp file as follows:

gen_vel                  = no; yes
gen_temp                 = 100
gen_seed                 = 1223
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl                   = berendsen  ; nose-hoover ;berendsen
; Groups to couple separately
tc-grps                  = protein
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1   
ref_t                    = 100  
; Pressure coupling     
Pcoupl                   =  no; 


The following is from my log file:

There are 1802 atoms in your xtc output selection

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------

   Energies (kJ/mol)
           Bond          Angle       G96Angle Ryckaert-Bell.
LJ-14
    2.23601e+03    3.10376e+02    9.73565e+02    4.90946e+03    3.92667e
+04
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic
En.
    3.73370e+03   -3.85288e+03   -3.22634e+03    4.43506e+04    1.21982e
+04
   Total Energy    Temperature Pressure (bar)
    5.65488e+04    5.43368e+02    0.00000e+00

           Step           Time         Lambda
              1        0.00200        0.00000


This is the first run after EM. I set "gen_vel = no" on purpose. When I
checked the trr file, the initial velocities were zeros, so that's
right. However, the log file showed that the initial KE and T were not
zeros. This confuses me. How does gromacs calculate KE and T? Another
strange thing is that the initial temperature is 500K, not 100K even
though I set ref_t =100. Any help will be highly appreciated!


All the best!


Dongsheng