Dear gromacs users<br><br>in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen)<br>-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)]<br><br>I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A.<br>
<br>and angle of 30 = acceptor-donor–hydrogen angle.<br><br>is my think true?<br><br>if I want following criterion for hydrogen bond analysis, is [ -r 3.5 and -a 135 ] true?<br><br><span style="font-size:12pt;font-family:"Times New Roman","serif";color:rgb(0, 0, 0)">donor-acceptor distance (d<sub>DA</sub>)
≤ 3.5 </span><span style="font-size:12pt;color:rgb(0, 0, 0)">Å</span><span style="font-size:12pt;font-family:"Times New Roman","serif";color:rgb(0, 0, 0)"><span> </span>and the donor–hydrogen-acceptor angle (α<sub>DHA</sub>)
≥ 135</span><span style="font-size:12pt;color:rgb(0, 0, 0)">°</span><span style="font-size:12pt;font-family:"Times New Roman","serif";color:rgb(0, 0, 0)">.</span><br><br>any help will highly appreciated.<br>
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