[gmx-users] about toplogy file

amit jain amitgood at gmail.com
Mon Apr 2 00:14:14 CEST 2007

Hello all,
I am trying to understand the topology file for gromacs.
so as to make n-alkane chain. for that I have dihedral parameters of
periodic type.
In the manual it says that

With the periodic GROMOS (dihedral ) potential a special 1-4 LJ-interaction
must be included;
for this reason I set gen-pairs = yes in [default]
in  [molecule type]
    name  nrexcl=2             (to take in to account 1-4 interaction)
and then again in  [pairs], I list down all 1-4 pairs,

I am wondering is it correct to do all three, or I am missing something.

thanks in advance,
I appreciate your reply,

Amit Jain
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