[gmx-users] system blowing

[Mark Abraham]

Ramachandran G wrote:
> Dear all,
>       I am trying to minimize a protein structure but i noticed 
> initially before it starts minimization, it gives warning
> -------------------------------------
> Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 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
> Using 10 BFGS correction steps.
> 
>    F-max             =  7.89523e+03 on atom 1185
>    F-Norm            =  4.87025e+04
>  ------------------------------
> finally it converged to machine precision but not to the requested 
> precision Fmax < 1000. When i view final structure, it
> looks the residues are sprayed out. The mdp file which i used for 
> minimization is

This .mdp does not match the above output.

> ------------------------------------------------------------------------------------
> Title               =   protien test
> cpp                 =  /lib/cpp
> ;include             =  -I../top
> define              = -DFLEXIBLE
> constraints         = none
> integrator          =  steep
> nstcomm             =  1
> dt                  =  0.002    ; ps !
> nsteps              =  50000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.4
> coulombtype         =  shift
> rcoulomb            =  1.2
> vdwtype             =  shift
> rvdw                =  1.2
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> 
> ------------------------------------------------------------
> 
> 
> This protein structure has been minimized using Charmm but in gromacs i 
> am having problem. Can anyone help me. Thank you.

There's so many things you might have done to it since leaving CHARMM 
that it's scarcely material that it was minimized there. Check your 
termini and the locations of your solvent molecules. It's impossible to 
help you further without more detail of your preparation.

Mark