[gmx-users] dummies...confused

[Senthil Kandasamy]

I generated a topolgy for a short peptide with the -dummies aromatics
option. the topology has the following section

________________________________________________________________________
[ dummies3 ]
;  ai    aj    ak    al funct            c0            c1            c2
    5     7     1     2    -4 
    6     7     1     2     4 
   35    30    31    32    -4 
   36    30    31    32     4 
   76    71    72    73    -4 
   77    71    72    73     4 
   91    86    87    88    -4 
   92    86    87    88     4 
  112   107   108   109    -4 
  113   107   108   109     4 
  127   122   123   124    -4 
  128   122   123   124     4 
  164   159   160   161    -4 
  165   159   160   161     4 
  210   205   206   207    -4 
  211   205   206   207     4 
  243   238   239   240    -4 
  244   238   239   240     4 
  258   253   254   255    -4 
  259   253   254   255     4 

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
_____________________________________________

I do not understand the negative values for the "funct" variable.

Also,is the first column in the dummies directive is the atom number of
the dummy to be constructed (with the atomname e.g. MNH3), or is it the
atom number of the hydrogen atoms beng dummyfied? 


Senthil