# [gmx-users] energy is coming "nan"

Tue Apr 6 14:56:04 CEST 2010

```Hi ,
I am trying to simulate a protein in vacuum for 10 ns.
However at around 8.8 ns the log file shows the following
Step           Time         Lambda
4411700     8823.40000        0.00000

Energies (kJ/mol)
Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
1.37934e+04    1.02343e+04    6.09706e+02    6.42224e+03    7.97160e+03
Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
4.08238e+04   -1.23373e+04   -1.31884e+05   -6.43660e+04    2.34001e+04
Total Energy    Temperature Pressure (bar)
-4.09659e+04    2.93347e+02    0.00000e+00

Large VCM(group rest):     -0.15115,     -0.85874,     -0.88165, Temp-cm:  3.61048e+00
Large VCM(group rest):     -3.30356,     -1.50152,    -11.40962, Temp-cm:  3.36602e+02
Group rest with mass  4.50563e+04, Ekrot  3.33396e+19 Det(I) =  4.98670e+95
COM:      4.40566       4.40778       4.74707
P:   -148846.33496  -67653.09375  -514075.76562
V:       -3.30356      -1.50152     -11.40962
J:   457896798773861765087232.00000  1805633659184017884315648.00000
86113127573044898824192.00000
w:       -0.00006       0.00002       0.00075
Inertia tensor (3x3):
Inertia tensor[    0]={ 7.62652e+36, -2.04805e+36, -9.25856e+37}
Inertia tensor[    1]={-2.04805e+36,  5.49988e+35,  2.48632e+37}
Inertia tensor[    2]={-9.25856e+37,  2.48632e+37,  1.12399e+39}
Large VCM(group rest):      0.16121,      0.70906,     46.02300, Temp-cm:  4.97490e+03
Group rest with mass  4.50563e+04, Ekrot  8.32461e+18 Det(I) = -9.80133e+94
COM:      4.35971       4.41628       4.51177
P:     7263.49854   31947.81250  2073627.46875
V:        0.16121       0.70906      46.02300
J:   58359181927255633821696.00000  -2981584234146221780893696.00000
7570244118347216060416.00000
w:        0.00002      -0.00001      -0.00026
Inertia tensor (3x3):
Inertia tensor[    0]={ 1.16144e+37, -3.11896e+36, -1.40998e+38}
Inertia tensor[    1]={-3.11896e+36,  8.37572e+35,  3.78640e+37}
Inertia tensor[    2]={-1.40998e+38,  3.78640e+37,  1.71171e+39}
Step           Time         Lambda
4411800     8823.60000        0.00000

Energies (kJ/mol)
Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
nan    9.22750e+06    0.00000e+00    1.80795e+04            nan
Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
nan            nan            nan            nan            nan
Total Energy    Temperature Pressure (bar)
nan            nan    0.00000e+00

After that the energy, temperature are coming as "nan".

The ".mdp" file that I have used is this:
integrator               = md
tinit                    = 0
dt                       = 0.002
nstcomm                  =1
comm_mode                = ANGULAR
nsteps                   = 5000000
nstxout                  = 100
nstvout                  = 500
nstfout                  = 0
nstlog                   = 100
nstenergy                = 10
nstxtcout                = 100
xtc-precision            = 100
energygrps               = PROTEIN
nstlist                  = 10
ns_type                  = simple
pbc                      = no
rlist                    = 0.0
domain-decomposition     = no
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0.0
epsilon-r                = 1
; Van der Waals =
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 0.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein
tau_t               =  0.1
ref_t               =  300
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  173529

What can be the reason for this?
Any suggestion regarding this will be very helpful.