<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; "><div style="font-family: 'times new roman', 'new york', times, serif; "><div dir="ltr" style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> </div> <br><div id="yiv560496282"><div><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; "><div style="color: rgb(0, 0, 0); font-size: 12pt; font-family: times, serif; ">Dear GROMACS users,</div><div style="color: rgb(0, 0, 0); font-size: 12pt; font-family: times, serif; ">I'm a novice user,</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman',
'new york', times, serif" size="3">I've been trying to find a way to visualize hydrogen bonds with VMD,but I haven't been </font><font face="'times new roman', 'new york', times, serif">successful.</font></div><div><font size="3">After running a simulation of 13 Hypericin molecules solved in Water, I loaded the.gro file and then the trajectory file .xtc, after that in the Create Representation window I changed to CPK and then modified to show just the Hypericin molecules (not water).Later I created another representation and </font>changed<font size="3"> to HBONDS and in the panel changed to "name H O",but VMD doesn't show the HBONDS formed between O and H atoms.</font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3">Where is my mistake?</font></div><div style="color: rgb(0, 0, 0);
font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3">Thanks in Advance</font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3"><br></font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3">Hovakim Grabski</font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3">Russian-Armenian(Slavonic) University</font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif"
size="3"><br></font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3"><br></font></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="'times new roman', 'new york', times, serif" size="3"> </font></div></div></div></div><br><br> </div> </div> </div></body></html>