[gmx-users] Brownian dynamics]

[Michel Fodje]

On Wed, 2002-02-13 at 21:50, David van der Spoel wrote:
> Further you could check the mdp file for strange options. Turn off
> everything like freezing restraining etc. Do also check the temperature
> you get (and the one you use for BD). Try normal MD, to see whether it is
> your conformation or the algorithm

I stripped down the mdp file to:

cpp            = /lib/cpp
integrator     = bd
dt             = 0.002
nsteps         = 50000
nstxout        = 500
nstvout        = 500
nstlog         = 500
nstenergy      = 25
energygrps     = Protein
lincs_order    = 8
tc_grps        = Protein
tau_t          = 0.1
ref_t          = 300
rlist          = 1.4 
rcoulomb       = 1.4
rvdw           = 1.4
pbc            = no


just changing the integrator to MD, everything works fine. However, with
BD I get the original error message with NaN energies:

step 0Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information


with -debug I got 4 other files, 3 plots and a HUGE! mdrun.log.  The
plots are attached. Somewhere down the mdrun.log were lots of:

 1-4 (2,6) interaction not within cut-off! r=2.82152. Ignored-0.828465
-0.481127 1.887176
1.106325 1.105578 3.174596
1-4 (2,9) interaction not within cut-off! r=2.81398. Ignored-2.208382
2.286521 2.627285
1.052079 0.906679 3.467846
1-4 (3,6) interaction not within cut-off! r=3.63883. Ignored-2.208382
2.286521 2.627285
...

Michel
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