[gmx-users] Brownian dynamics

[Michel Fodje]

Hi,
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



   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


I am using the Gromos96 Vacuum force field ffG43b1 and my bd.mdp file is
as follows:


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


Any help with what I may be doing wrong is highly appreciated.


Michel
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