[gmx-users] weird mdrun...using gromacs 3.3.3
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 8 06:00:33 CEST 2009
Naga Rajesh Tummala wrote:
> 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)"
IIRC "nrdf" is short for "number of degrees of freedom" which in turn
suggests that the number of constraints has changed between the files,
but I don't know if that's consistent with all other .tpr entries being
identical.
Did you make these .tpr files with different .mdp files? Different
GMXLIB values? Different GROMACS installations?
Mark
> 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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>>>
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