[gmx-users] re: n-hexadecane simulation

[chris.neale at utoronto.ca]

You have #2 in the 3rd column which nmeans that you are not excluding  
1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change  
this value to a one instead of a two. That should fix your problem.  
However, I would recommend that you set up the regular RB bonds like  
this. That way you have the settings in case you want to stop  
constraining bond lengths.

Remove your [ constraints ] section and adding this:

[ bonds ]
     1    2      1   0.15300E+00 0.33470E+06
     2    3      1   0.15300E+00 0.33470E+06
     3    4      1   0.15300E+00 0.33470E+06
     4    5      1   0.15300E+00 0.33470E+06
     5    6      1   0.15300E+00 0.33470E+06
     6    7      1   0.15300E+00 0.33470E+06
     7    8      1   0.15300E+00 0.33470E+06
     8    9      1   0.15300E+00 0.33470E+06
     9   10      1   0.15300E+00 0.33470E+06
    10   11      1   0.15300E+00 0.33470E+06
    11   12      1   0.15300E+00 0.33470E+06
    12   13      1   0.15300E+00 0.33470E+06
    13   14      1   0.15300E+00 0.33470E+06
    14   15      1   0.15300E+00 0.33470E+06
    15   16      1   0.15300E+00 0.33470E+06


Chris.