<div>Hello all,</div>
<div>I am trying to understand the topology file for gromacs.</div>
<div>so as to make n-alkane chain. for that I have dihedral parameters of periodic type.<br clear="all">In the manual it says that<font face="NimbusRomNo9L-Regu" size="3">
<p align="left">With the periodic GROMOS (dihedral ) potential a special 1-4 LJ-interaction must be included;</p></font>for this reason I set gen-pairs = yes in [default]</div>
<div>in [molecule type] </div>
<div> name nrexcl=2 (to take in to account 1-4 interaction) </div>
<div>and then again in [pairs], I list down all 1-4 pairs, </div>
<div> </div>
<div>I am wondering is it correct to do all three, or I am missing something.</div>
<div> </div>
<div>thanks in advance,</div>
<div>I appreciate your reply,</div>
<div> </div>
<div>Amit Jain</div>