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<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>
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<font size="3" face="'times new roman',
'new york', times, serif">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>
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<font size="3" face="'times new roman', 'new york', times, serif">Where is my mistake?</font></div>
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<font size="3" face="'times new roman', 'new york', times, serif">Thanks in Advance</font></div>
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<font size="3" face="'times new roman', 'new york', times, serif">Hovakim Grabski</font></div>
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<font size="3" face="'times new roman', 'new york', times, serif">Russian-Armenian(Slavonic) University</font></div>
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<font size="3" face="'times new roman', 'new york', times, serif">I think you should refer to VMD mailing list. However, as far as I know you should create representation:<br>
all not water<br>
and set to HBONDS<br>
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Jan<br>
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