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
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