[gmx-users] peptide disappeared

[Wang Zhun]

Hello, all,
I met with a strange problem during MD simulation of a peptide in vacuum:
the peptide disappeared after 4ns.
Can  anyone explain this?
Thanks!

The follwing are my md.mdp and part of md.log:

title                    =
cpp                      = /lib/cpp
include                  =
define                   =
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000000
init_step                = 0
comm_mode                = none
nstcomm                  = -1
nstxout                  = 1000
nstcheckpoint            = 0
nstlog                   = 1000
nstenergy                = 0
nstxtcout                = 0
xtc-precision            = 1000
nstlist                  = 10
ns_type                  = simple
pbc                      = no
rlist                    = 1
domain-decomposition     = no
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.0
DispCorr                 = No
table-extension          = 1
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes
gen_vel                  = no
gen-temp                 = 300
gen-seed                 = 173529
constraints              = none





	   Step           Time         Lambda
        2210000     4420.00000        0.00000

   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    2.00119e+02    9.57417e+01    8.23339e+01    3.42419e+01    4.97098e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
    2.90042e+03   -6.87585e+02   -3.27700e+03   -6.02028e+02    4.51762e+02
   Total Energy    Temperature Pressure (bar)
   -1.50266e+02    1.71672e+02    0.00000e+00

           Step           Time         Lambda
        2211000     4422.00000        0.00000

   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
            nan            nan            nan            nan            nan
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
            nan    0.00000e+00    0.00000e+00            nan            nan
   Total Energy    Temperature Pressure (bar)
            nan            nan    0.00000e+00

           Step           Time         Lambda
        2212000     4424.00000        0.00000

   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
            nan            nan            nan            nan            nan
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
            nan    0.00000e+00    0.00000e+00            nan            nan
   Total Energy    Temperature Pressure (bar)
            nan            nan    0.00000e+00