[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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