[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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