Hi , <br />
I am trying to simulate a protein in vacuum for 10 ns.<br />
However at around 8.8 ns the log file shows the following<br />
Step Time Lambda<br />
4411700 8823.40000 0.00000<br />
<br />
Energies (kJ/mol)<br />
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14<br />
1.37934e+04 1.02343e+04 6.09706e+02 6.42224e+03 7.97160e+03<br />
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.<br />
4.08238e+04 -1.23373e+04 -1.31884e+05 -6.43660e+04 2.34001e+04<br />
Total Energy Temperature Pressure (bar)<br />
-4.09659e+04 2.93347e+02 0.00000e+00<br />
<br />
Large VCM(group rest): -0.15115, -0.85874, -0.88165, Temp-cm: 3.61048e+00<br />
Large VCM(group rest): -3.30356, -1.50152, -11.40962, Temp-cm: 3.36602e+02<br />
Group rest with mass 4.50563e+04, Ekrot 3.33396e+19 Det(I) = 4.98670e+95<br />
COM: 4.40566 4.40778 4.74707<br />
P: -148846.33496 -67653.09375 -514075.76562<br />
V: -3.30356 -1.50152 -11.40962<br />
J: 457896798773861765087232.00000 1805633659184017884315648.00000 <br />
86113127573044898824192.00000<br />
w: -0.00006 0.00002 0.00075<br />
Inertia tensor (3x3):<br />
Inertia tensor[ 0]={ 7.62652e+36, -2.04805e+36, -9.25856e+37}<br />
Inertia tensor[ 1]={-2.04805e+36, 5.49988e+35, 2.48632e+37}<br />
Inertia tensor[ 2]={-9.25856e+37, 2.48632e+37, 1.12399e+39}<br />
Large VCM(group rest): 0.16121, 0.70906, 46.02300, Temp-cm: 4.97490e+03<br />
Group rest with mass 4.50563e+04, Ekrot 8.32461e+18 Det(I) = -9.80133e+94<br />
COM: 4.35971 4.41628 4.51177<br />
P: 7263.49854 31947.81250 2073627.46875<br />
V: 0.16121 0.70906 46.02300<br />
J: 58359181927255633821696.00000 -2981584234146221780893696.00000 <br />
7570244118347216060416.00000<br />
w: 0.00002 -0.00001 -0.00026<br />
Inertia tensor (3x3):<br />
Inertia tensor[ 0]={ 1.16144e+37, -3.11896e+36, -1.40998e+38}<br />
Inertia tensor[ 1]={-3.11896e+36, 8.37572e+35, 3.78640e+37}<br />
Inertia tensor[ 2]={-1.40998e+38, 3.78640e+37, 1.71171e+39}<br />
Step Time Lambda<br />
4411800 8823.60000 0.00000<br />
<br />
Energies (kJ/mol)<br />
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14<br />
nan 9.22750e+06 0.00000e+00 1.80795e+04 nan<br />
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.<br />
nan nan nan nan nan<br />
Total Energy Temperature Pressure (bar)<br />
nan nan 0.00000e+00<br />
<br />
After that the energy, temperature are coming as "nan".<br />
<br />
The ".mdp" file that I have used is this:<br />
integrator = md<br />
tinit = 0<br />
dt = 0.002<br />
nstcomm =1<br />
comm_mode = ANGULAR<br />
nsteps = 5000000<br />
nstxout = 100<br />
nstvout = 500<br />
nstfout = 0<br />
nstlog = 100<br />
nstenergy = 10<br />
nstxtcout = 100<br />
xtc-precision = 100<br />
energygrps = PROTEIN<br />
nstlist = 10<br />
ns_type = simple<br />
pbc = no<br />
rlist = 0.0<br />
domain-decomposition = no<br />
coulombtype = Cut-off<br />
rcoulomb-switch = 0<br />
rcoulomb = 0.0<br />
epsilon-r = 1<br />
; Van der Waals =<br />
vdw-type = Cut-off<br />
rvdw-switch = 0<br />
rvdw = 0.0<br />
; Berendsen temperature coupling is on in two groups<br />
Tcoupl = berendsen<br />
tc-grps = Protein<br />
tau_t = 0.1<br />
ref_t = 300<br />
; Generate velocites is off at 300 K.<br />
gen_vel = yes<br />
gen_temp = 300<br />
gen_seed = 173529<br />
<br />
What can be the reason for this?<br />
Any suggestion regarding this will be very helpful.<br />
Thanks in advance<br />
Sarbani<br><Table border=0 Width=644 Height=57 cellspacing=0 cellpadding=0 style="font-family:Verdana;font-size:11px;line-height:15px;"><TR><td><A HREF="http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?" target="_blank"><IMG SRC="http://sigads.rediff.com/RealMedia/ads/adstream_nx.ads/www.rediffmail.com/signatureline.htm@Middle"></A></td></TR></Table>