[gmx-users] MD run error

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 12 02:37:08 CEST 2006

Kushal Seth wrote:
> Hi all !
> I am running a MD simulation and i got

You appear to be trying to do an energy minimization, which although 
often able to be done by the same code as molecular dynamics, is 
inherently non-dynamical. Hence it's unwise to confuse matters by 
referring to one as "MD". See section 1 of the gromacs manual.

> "Warning: 1-4 interaction between 1 and 6 at distance 1.102 which is
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file"

It's probably right about that. Look at 1 and 6 in the initial structure 
and see what you think they should do. Then look at the output of the EM 
and see what they have done. This may suggest where the problem lies.

>  and then EM process goes and terminates at 26 th steps saying that
> "Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 100
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> writing lowest energy coordinates.
> Steepest Descents converged to machine precision in 26 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -6.0066115e+23
> Maximum force     =  1.8847882e+25 on atom 2502
> Norm of force     =  5.5707627e+25".
> I have tried changing the sizes and pressure couplings.Thats does not help.

Pressure coupling can only be applied to a dynamical simulation, so this 
cannot help at all.

Check your input structure, your topology, the output structure and your 
input .mdp file. If the former are all OK and you can't see anything 
wrong with the .mdp file, include it in a message here.


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