[gmx-users] 1-4 interaction warning

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 9 15:20:52 CEST 2009


David Wright wrote:
> Dear GROMACS users,
> 
> 
> 
>   When I started to run a simulation with GROMACS 4.0.4, I got a
> warning message as following at the beginning and the simulation
> crashed immediately:
> 
> 
> 
> Warning: 1-4 interaction between 64 and 73 at distance 15.455 which is larger than the 1-4 table size 2.400 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
> 
> or with user tables increase the table size
> 
> 
> 
>    I checked the input .gro file and found the records of atoms No. 64 and 73 as following:
> 
> 
> 
>     2LEU      C   64   5.193   4.146   3.768 -0.5041  0.1368 -0.6462
> 
>     3MET      C   73   5.093   3.917   3.953 -0.3002 -1.2581 -0.2382
> 
> 
> 
> The distance 15.455 nm in the warning message is much larger than the
> real distance between the two atoms shown above. Actually it is very
> close to the z-axis cubic box vector, which is 15.268 nm in my
> simulation. So I doubt that GROMACS might make a mistake by calculating
> the distance between one atom and the periodic image of the other atom.
> 
> One
> special aspect of atom No. 73 is that I applied angle restrains on this
> atom and a few others. If I remove the angle restrains, the problem will disappear. However, for some purpose, I need to keep the angle restrains
> in the simulation.

Since your system is exploding with the angle restraints and not 
otherwise, it seems likely you've done something wrong in implementing 
these. Check out the relevant manual sections, and/or post the relevant 
details here.

Mark

>    Does anyone have some idea to fix this problem of 1-4 interaction?
> 
> 
> 
>    Thank you very much!
> 
> 
> 
>         Best Regards,
>            David Wright
> 
> 
> 
> 
>       
> 
> 
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> 
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