[gmx-users] peptide disappeared
Wang Zhun
wangzhun at pumc.edu.cn
Mon Sep 26 08:58:41 CEST 2005
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
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