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<div>Dear Gmx's, </div>
<div>I am trying to get an infinite DNA chain to work. I was following an earlier discussion:</div>
<div><a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html" target="_blank">https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html</a></div>
<div>I got pdb2gmx to accept my lose ends and also added bonds, angles and dihedrals to the topology file connection both ends. But after a short simulation it looks like the the force is calculated over the "real" distance and not across the periodic boundary. It looks like there is a short gap in the DNA when I display the periodic image as well. </div>
<div>How does Gromacs determine, which is the correct bond direction/length? </div>
<div>Or how can I check for sure if the correct bond length is used? Would the simulation even start, if there is a bond stretching over 40 bais pairs?</div>
<div>I appreciate any advice very much!</div>
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<div>Best,</div>
<div>Roman</div>
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