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Hi,
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I'm studying the diffusion of metal ions into a protein active site and would like to run a brownian dynamics simulation with gromacs. However, I get the following output as soon as I start the simulation
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<PRE> Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
nan nan nan nan 0.00000e+00
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.
0.00000e+00 0.00000e+00 0.00000e+00 nan nan
Total Energy Temperature Pressure (bar)
nan nan 0.00000e+00
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I am using the Gromos96 Vacuum force field ffG43b1 and my bd.mdp file is as follows:
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<PRE>cpp                                = /lib/cpp
define                                =
integrator                        = bd
dt                         = 1.000
nsteps                                = 500000
nstxout                                = 5000
nstvout                                = 5000
nstlog                                = 5000
nstenergy                        = 250
energygrps                        = Protein ZN2
bd_temp                                = 300
bd_fric                                = 0
ld_seed                         = 173529
tc_grps                                = Protein ZN2
tau_t                                = 0.1 0.1
ref_t                                = 300 300
nstlist                                = 10
ns_type                                = grid
constraint_algorithm                = lincs
lincs_order                        = 8
coulombtype                        = cut-off
rvdw                                = 1.4
rlist                         = 1.4
rcoulomb                        = 1.4
pbc                                = no
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Any help with what I may be doing wrong is highly appreciated.
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Michel
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