<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span></span></div><div>Hi everyone, <br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div id="yiv1106543527"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div>I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step:</div><div><div>Na+ were added by replacing a solvent molecule at ca. 6 Å</div><div>from the phosphorus in the direction of the bisector of the angle</div><div>∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging</div><div>oxygen atoms)</div><div>I think what it means is that Na+ was added in a distance of
6 Å from the phosphorus. How can we specify this in GROMACS?</div><div><br></div><div>there is no such option in genion tool in gromacs package.</div><div><br></div><div> Thank you</div><div> B.Mehrazma</div></div></div></div></div><br><br> </div> </div> </div></body></html>