[gmx-users] weird mdrun...using gromacs 3.3.3
Naga Rajesh Tummala
rajesh.tnr at gmail.com
Tue Sep 8 06:28:09 CEST 2009
Dear Mark,
Some groups which were constrained in all 3 dimensions in one .mdp whereas
in other .mdp that groups were not constrained in x-direction.
But now I used same .mdp file and now even "nrdf" are same.
Strangely (common atleast when doing this simulation), the total energy and
other thermodynamics quantities were "nan" before but now they show some
huge number.
One thing I observed is the simulation runs fine only once (esp. first
time), but throws up error innumerous times after that.
I am using the same GROMACS built, same .mdp file and same values for GMXLIB
(I never changed them so far)
Below are the comparison of thermodynamic comparsions
LJ (SR) step 0: 103090, step 0: 4.7561e+18
Potential step 0: -707489, step 0: 4.7561e+18
Kinetic En. step 0: 1468.08, step 0: 1.02499e+35
Total Energy step 0: -706021, step 0: 1.02499e+35
Temperature step 0: 4.35424, step 0: 3.04006e+32
Pressure (bar) step 0: -3712.49, step 0: 2.73697e+33
Vir-XX step 0: 44045.4, step 0: -5.41605e+20
Vir-XY step 0: -2748.83, step 0: 1.41247e+20
Vir-XZ step 0: 1057.24, step 0: 4.23707e+20
Vir-YX step 0: -2800.27, step 0: 1.41247e+20
Vir-YY step 0: 46710.7, step 0: -1.87114e+20
Vir-YZ step 0: 2599.8, step 0: 1.39343e+19
Vir-ZX step 0: 1091.55, step 0: 4.23708e+20
Vir-ZY step 0: 2549.65, step 0: 1.39336e+19
Vir-ZZ step 0: 49744.6, step 0: -2.84725e+21
Pres-XX (bar) step 0: -3489.58, step 0: 1.70507e+33
Pres-XY (bar) step 0: 219.836, step 0: -5.38913e+32
Pres-XZ (bar) step 0: -84.925, step 0: -2.37631e+33
Pres-YX (bar) step 0: 223.957, step 0: -5.38913e+32
Pres-YY (bar) step 0: -3703.21, step 0: 2.67507e+32
Pres-YZ (bar) step 0: -208.473, step 0: 6.2505e+32
Pres-ZX (bar) step 0: -87.6739, step 0: -2.37631e+33
Pres-ZY (bar) step 0: -204.455, step 0: 6.2505e+32
Pres-ZZ (bar) step 0: -3944.69, step 0: 6.23832e+33
#Surf*SurfTen step 0: -2141.58, step 0: 3.22932e+34
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: 1.42541e+18
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11
T-System step 0: 4.35424, step 0: 3.04006e+32
*previously*
LJ (SR) step 0: 103090, step 0: nan
Potential step 0: -707489, step 0: nan
Kinetic En. step 0: 1468.08, step 0: nan
Total Energy step 0: -706021, step 0: nan
Temperature step 0: 4.35424, step 0: nan
Pressure (bar) step 0: -3712.49, step 0: nan
Vir-XX step 0: 44045.4, step 0: nan
Vir-XY step 0: -2748.83, step 0: nan
Vir-XZ step 0: 1057.24, step 0: nan
Vir-YX step 0: -2800.27, step 0: nan
Vir-YY step 0: 46710.7, step 0: nan
Vir-YZ step 0: 2599.8, step 0: nan
Vir-ZX step 0: 1091.55, step 0: nan
Vir-ZY step 0: 2549.65, step 0: nan
Vir-ZZ step 0: 49744.6, step 0: nan
Pres-XX (bar) step 0: -3489.58, step 0: nan
Pres-XY (bar) step 0: 219.836, step 0: nan
Pres-XZ (bar) step 0: -84.925, step 0: nan
Pres-YX (bar) step 0: 223.957, step 0: nan
Pres-YY (bar) step 0: -3703.21, step 0: nan
Pres-YZ (bar) step 0: -208.473, step 0: nan
Pres-ZX (bar) step 0: -87.6739, step 0: nan
Pres-ZY (bar) step 0: -204.455, step 0: nan
Pres-ZZ (bar) step 0: -3944.69, step 0: nan
#Surf*SurfTen step 0: -2141.58, step 0: nan
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
T-System step 0: 4.35424, step 0: nan
Thanks
Rajesh
On Mon, Sep 7, 2009 at 11:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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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