[gmx-users] weird mdrun...using gromacs 3.3.3
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 8 12:23:18 CEST 2009
Naga Rajesh Tummala wrote:
> 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
>
It looks to me like you have severe atomic overlap between these two systems
(and hence the astronomically large values for short-range nonbonded
parameters). Have you done any sort of energy minimization and equilibration on
this system?
-Justin
> Thanks
> Rajesh
>
>
> On Mon, Sep 7, 2009 at 11:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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 <mailto: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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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