[gmx-users] weird mdrun...using gromacs 3.3.3
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 8 04:07:52 CEST 2009
Naga Rajesh Tummala wrote:
> 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.
That seems intrinsically impossible. Please use gmxcheck to compare your
input and output files and report back.
Mark
> 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
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users
mailing list