[gmx-users] Brownian dynamics]

[Anton Feenstra]

Michel Fodje wrote:
> 
> I tried a timestep of 0.005 but the result was the same.  Even 0.001 did
> not help.

That is already indicating a problem in the starting structure...

> Maybe I should mention that I also get a warning at the beginning which
> says
> 
> 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

That is a pretty undeniable indication that there is something
seriously wrong with your starting structure: the 'outer' two atoms
of a series of four bonded atoms (A1 and A4 in A1-A2-A3-A4) should
normally be no further than 3 times your average bondlength apart,
say roughly 3*0.15 nm = 0.45 nm, not nearly 1 nm...

> after which the simulation continues, but with NaN energies in the
> output file

Figures...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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