[gmx-users] weird mdrun...using gromacs 3.3.3
Naga Rajesh Tummala
rajesh.tnr at gmail.com
Mon Sep 7 22:09:41 CEST 2009
Dear All,
Two simulations runs starting from same initial configuration results in
very different energies in the first step. Both are identical simulations,
nothing is changed.
Did anybody encounter such problem before ? If yes, can you let me know what
to do to fix this problem.
Below are the energy outputs from 2 simulation runs. First one ran smoothly
for 5000 time steps where as second one crashed after 0th step.
>From Run 1:
time: 0.00000e+00 step: 0
Component Energy Av. Energy Sum Energy
Bond 5.57798e+03 0.00000e+00 5.57798e+03
Angle 5.60521e+03 0.00000e+00 5.60521e+03
Proper Dih. 2.45557e+03 0.00000e+00 2.45557e+03
LJ-14 3.58007e+03 0.00000e+00 3.58007e+03
Coulomb-14 -9.18661e+02 0.00000e+00 -9.18661e+02
LJ (SR) 1.03090e+05 0.00000e+00 1.03090e+05
Disper. corr. -1.44859e+03 0.00000e+00 -1.44859e+03
Coulomb (SR) -7.52008e+05 0.00000e+00 -7.52008e+05
Coul. recip. -7.34228e+04 0.00000e+00 -7.34228e+04
Potential -7.07489e+05 0.00000e+00 -7.07489e+05
Kinetic En. 1.46808e+03 0.00000e+00 1.46808e+03
Total Energy -7.06021e+05 0.00000e+00 -7.06021e+05
Temperature 4.35424e+00 0.00000e+00 4.35424e+00
Pressure (bar) -3.71249e+03 0.00000e+00 -3.71249e+03
Vir-XX 4.40454e+04 0.00000e+00 4.40454e+04
Vir-XY -2.74883e+03 0.00000e+00 -2.74883e+03
Vir-XZ 1.05724e+03 0.00000e+00 1.05724e+03
Vir-YX -2.80027e+03 0.00000e+00 -2.80027e+03
Vir-YY 4.67107e+04 0.00000e+00 4.67107e+04
Vir-YZ 2.59980e+03 0.00000e+00 2.59980e+03
Vir-ZX 1.09155e+03 0.00000e+00 1.09155e+03
Vir-ZY 2.54965e+03 0.00000e+00 2.54965e+03
Vir-ZZ 4.97446e+04 0.00000e+00 4.97446e+04
Pres-XX (bar) -3.48958e+03 0.00000e+00 -3.48958e+03
Pres-XY (bar) 2.19836e+02 0.00000e+00 2.19836e+02
Pres-XZ (bar) -8.49250e+01 0.00000e+00 -8.49250e+01
Pres-YX (bar) 2.23957e+02 0.00000e+00 2.23957e+02
Pres-YY (bar) -3.70321e+03 0.00000e+00 -3.70321e+03
Pres-YZ (bar) -2.08473e+02 0.00000e+00 -2.08473e+02
Pres-ZX (bar) -8.76739e+01 0.00000e+00 -8.76739e+01
Pres-ZY (bar) -2.04455e+02 0.00000e+00 -2.04455e+02
Pres-ZZ (bar) -3.94469e+03 0.00000e+00 -3.94469e+03
#Surf*SurfTen -2.14158e+03 0.00000e+00 -2.14158e+03
Mu-X -3.94890e+03 0.00000e+00 -3.94890e+03
Mu-Y 8.47297e+00 0.00000e+00 8.47297e+00
Mu-Z 3.71283e+02 0.00000e+00 3.71283e+02
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00 1.65804e+04
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00 -4.43681e+03
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00 -9.18661e+02
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00 3.58007e+03
*LJ-SR:FMN-CNT -5.88918e+02 0.00000e+00 -5.88918e+02*
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00 -8.47612e+04
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00 4.93246e+02
LJ-SR:FMN-CMT -5.58573e+02 0.00000e+00 -5.58573e+02
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00 -2.41537e+04
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00 -4.60796e+03
LJ-SR:CNT-SOD -1.15710e+00 0.00000e+00 -1.15710e+00
LJ-SR:CNT-SOL -3.05429e+02 0.00000e+00 -3.05429e+02
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00 2.04577e+04
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00 -2.29117e+01
LJ-SR:SOD-CMT -7.17905e-01 0.00000e+00 -7.17905e-01
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00 -1.84476e+04
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00 1.89181e+03
LJ-SR:CMT-SOL -3.13823e+02 0.00000e+00 -3.13823e+02
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00 -6.61683e+05
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00 1.11541e+05
T-System 4.35424e+00 0.00000e+00 4.35424e+00
Xi-System 0.00000e+00 0.00000e+00 0.00000e+00
>From Run 2:
time: 0.00000e+00 step: 0
Component Energy Av. Energy Sum Energy
Bond 5.57798e+03 0.00000e+00 5.57798e+03
Angle 5.60521e+03 0.00000e+00 5.60521e+03
Proper Dih. 2.45557e+03 0.00000e+00 2.45557e+03
LJ-14 3.58007e+03 0.00000e+00 3.58007e+03
Coulomb-14 -9.18661e+02 0.00000e+00 -9.18661e+02
LJ (SR) 4.75610e+18 0.00000e+00 4.75610e+18
Disper. corr. -1.44859e+03 0.00000e+00 -1.44859e+03
Coulomb (SR) -7.52008e+05 0.00000e+00 -7.52008e+05
Coul. recip. -7.34228e+04 0.00000e+00 -7.34228e+04
Potential 4.75610e+18 0.00000e+00 4.75610e+18
Kinetic En. 1.17875e+35 0.00000e+00 1.17875e+35
Total Energy 1.17875e+35 0.00000e+00 1.17875e+35
Temperature 3.44094e+32 0.00000e+00 3.44094e+32
Pressure (bar) 3.14754e+33 0.00000e+00 3.14754e+33
Vir-XX -5.41605e+20 0.00000e+00 -5.41605e+20
Vir-XY 1.41247e+20 0.00000e+00 1.41247e+20
Vir-XZ 4.23707e+20 0.00000e+00 4.23707e+20
Vir-YX 1.41247e+20 0.00000e+00 1.41247e+20
Vir-YY -1.87114e+20 0.00000e+00 -1.87114e+20
Vir-YZ 1.39343e+19 0.00000e+00 1.39343e+19
Vir-ZX 4.23708e+20 0.00000e+00 4.23708e+20
Vir-ZY 1.39336e+19 0.00000e+00 1.39336e+19
Vir-ZZ -2.84725e+21 0.00000e+00 -2.84725e+21
Pres-XX (bar) 2.93679e+33 0.00000e+00 2.93679e+33
Pres-XY (bar) -5.38913e+32 0.00000e+00 -5.38913e+32
Pres-XZ (bar) -2.37631e+33 0.00000e+00 -2.37631e+33
Pres-YX (bar) -5.38913e+32 0.00000e+00 -5.38913e+32
Pres-YY (bar) 2.67507e+32 0.00000e+00 2.67507e+32
Pres-YZ (bar) 6.25050e+32 0.00000e+00 6.25050e+32
Pres-ZX (bar) -2.37631e+33 0.00000e+00 -2.37631e+33
Pres-ZY (bar) 6.25050e+32 0.00000e+00 6.25050e+32
Pres-ZZ (bar) 6.23832e+33 0.00000e+00 6.23832e+33
#Surf*SurfTen 2.85064e+34 0.00000e+00 2.85064e+34
Mu-X -3.94890e+03 0.00000e+00 -3.94890e+03
Mu-Y 8.47297e+00 0.00000e+00 8.47297e+00
Mu-Z 3.71283e+02 0.00000e+00 3.71283e+02
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00 1.65804e+04
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00 -4.43681e+03
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00 -9.18661e+02
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00 3.58007e+03
* LJ-SR:FMN-CNT 2.06986e+18 0.00000e+00 2.06986e+18*
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00 -8.47612e+04
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00 4.93246e+02
LJ-SR:FMN-CMT 1.26082e+18 0.00000e+00 1.26082e+18
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00 -2.41537e+04
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00 -4.60796e+03
LJ-SR:CNT-SOD 3.29985e+12 0.00000e+00 3.29985e+12
LJ-SR:CNT-SOL 1.42541e+18 0.00000e+00 1.42541e+18
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00 2.04577e+04
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00 -2.29117e+01
LJ-SR:SOD-CMT 5.87209e+11 0.00000e+00 5.87209e+11
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00 -1.84476e+04
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00 1.89181e+03
LJ-SR:CMT-SOL -3.13899e+02 0.00000e+00 -3.13899e+02
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00 -6.61683e+05
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00 1.11541e+05
T-System 3.44094e+32 0.00000e+00 3.44094e+32
Xi-System 0.00000e+00 0.00000e+00 0.00000e+00
Thanks a lot
Any help is greatly appreciated.
Thanks
Rajesh
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