[gmx-users] question about topologies

Marcello Cammarata marcello.cammarata at unipa.it
Tue Oct 21 18:30:20 CEST 2014

i am studied the capter 5 about topology, and o did not understand  
some aspect:
1-in the a.tp file, what does means the number after the simbol?

0   15.999 (C==0)
OM  15.99  (CO)
C   12.01  (C=0, C-N)

2- witch differences are between O and C?

3- The file with the virtual sites what estention need to have?

4- in the manual is presented a case of a rtp file of [GLY] according  
with the structure that is C2H5NO2
   so questions are:
   a) there is a -C in the last row. Is this C part of the molecule?
   b) Why the group CH2 is called CA?
   c) What differences are between C and O, if both are C=0?

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