[gmx-users] problem with energy minimization

[Mark Abraham]

sanjay23 at iitb.ac.in wrote:
> dear gromacs user
> i am doing simulation of Gal1p protein with ligand and without ligand.i
> made the system without ligand by removing the ligand from pdb file then i
> use pdb2gmx for generating topology file and editconf for adding box
> dimention and add spc water molecules.i have not face any problem up to
> grompp but when i did energy minimization of system i got this warning:-
> "Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 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"
> but em is comleted with machine precession with -ve energy,

Hmm? If you got this warning during EM, it seems most unlikely you'd 
converge that EM, or that you should trust the resulting structure to be 
a minimum.

>  i added
> table-extention (1.1nm)in mdp file, and got same warning.even i don't what
> affect done on system by adding table-extention.I am also getting same
> problem  with ligand.kidnely help me
> sanjay

Justin's advice last time still applies... see 
http://www.gromacs.org/pipermail/gmx-users/2008-May/034017.html This 
kind of error arises in EM because you have some serious problem with 
your starting structure, topology or both. Visualize your starting 
structure, and/or along the EM "trajectory" to see which part of your 
structure is causing the problem when. Atoms 2779 and 2788 are a good 
start, but they might be the symptom and not the cause.

Mark