[gmx-users] Dimer simulations using Gromacs

Monika Sharma mon_sharma at research.iiit.ac.in
Wed Dec 26 07:55:01 CET 2007

Dear All,
I wish to do some simulations using dimer of protein. I have generated 
.gro file for that. I am able to minimize structure, but when I am 
trying to give it for equilibration run. I am getting error as:
"Warning: 1-4 interaction between 5786 and 5791 at distance 5.468 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"

On looking the gro file it seems that these atom numbers corresponds to 
two different chains of the dimer. But it is trying to map it as one 
protein molecule instead of two as can be seen from the topol.top file.

[ molecules ]
; Compound        #mols
Protein             1
FAD                 1
NAD                 1
FAD                 1
NAD                 1
SOL             123000

My question is that is it normal for gromacs to read dimer as single 
unit in .gro file. Or do I need to make some modifications in .gro and 
.top file to make it read as two entities. Suggestions are required for 

Thanking you,

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