[gmx-users] 1-4 interaction warning

David Wright davidwrightem at yahoo.com
Wed Sep 9 15:04:48 CEST 2009

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.

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.

   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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