<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear GROMACS users,<br>
<br>
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:<br>
<br>
Warning: 1-4 interaction between 64 and 73 at distance 15.455 which is larger than the 1-4 table size 2.400 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
<br>
I checked the input .gro file and found the records of atoms No. 64 and 73 as following:<br>
<br>
2LEU C 64 5.193 4.146 3.768 -0.5041 0.1368 -0.6462<br>
3MET C 73 5.093 3.917 3.953 -0.3002 -1.2581 -0.2382<br>
<br>
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.<br><br>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.<br>
<br>
Does anyone have some idea to fix this problem of 1-4 interaction?<br>
<br>
Thank you very much!<br>
<br>
Best Regards,<br> David Wright<br><br></td></tr></table><br>