[gmx-users] weird mdrun...using gromacs 3.3.3
Naga Rajesh Tummala
rajesh.tnr at gmail.com
Tue Sep 8 05:49:00 CEST 2009
Dear Mark,
When I compare the .tpr files the following is the online line where its
different
"inputrec->grpopts.nrdf[0] (8.240200e+04 - 8.110200e+04)"
When I compare two energy files,
"LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18
LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18
LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12
LJ-SR:CNT-SOL step 0: -305.429, step 0: nan
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11
LJ-SR:CMT-SOL step 0: -313.823, step 0: nan"
The total energies and also the virial, pressure, surface tension and other
thermodynamics quantities are different.
When I compare .trr files, there is no difference between two files in the
initial step.
I personally felt that there was something wrong with the force field files,
but I could not find anything there.
Thanks
Rajesh
On Mon, Sep 7, 2009 at 9:07 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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