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<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>Hi all,<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>I am
trying to caluculate number of hydrogen bond in my system using the following
command:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>g_hbond
-f model_frame2000.pdb -s md.tpr -n index_water.ndx -num hbnum.xvg <o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>Where
the file model_frame2000.pdb is the coordinate from a frame during my MD
simulation, and the index file </span></font><font size=3 face=宋体><span
style='font-size:12.0pt;font-family:宋体'>（</span></font><font size=3><span
lang=EN-US style='font-size:12.0pt'>index_water.ndx</span></font><font size=3
face=宋体><span style='font-size:12.0pt;font-family:宋体'>）</span></font><font
size=3><span lang=EN-US style='font-size:12.0pt'> contains the index six
adjacent tip5p water molecules, see following:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>2559
2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505 3506 3507 3508 <o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>5354
5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050 6051 6052 6053 <o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>The arrangement
of water oxygen is like this (rectangle), which “ - ” indicates the distance is
less than 0.35 nm.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>OW - OW
- OW<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'> |
| |<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>OW - OW
- OW<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>The
output hbnum.xvg gives<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@TYPE
xy<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@ view
0.15, 0.15, 0.75, 0.85<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@
legend on<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@
legend box on<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@
legend loctype view<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@
legend 0.78, 0.8<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@
legend length 2<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@ s0
legend "Hydrogen bonds"<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>@ s1
legend "Pairs within 0.35 nm"<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>
-1
4 10<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>As I
know, the 2nd column is the number of Hydrogen bonds, and the 3ird column
indicates “the Pairs within 0.35 nm, but with angle > <st1:chmetcnv TCSC="0"
NumberType="1" Negative="False" HasSpace="False" SourceValue="30" UnitName="”"
w:st="on">30”</st1:chmetcnv>. After viewing the stucture in VMD, I found that
the number of Hydrogen bond seems to be correct. However, only 7 pairs of
water oxygen within 0.35 nm can be found (see above for the schematic drawing
of water arrangement), thus “the Pairs within 0.35 nm, but with angle > <st1:chmetcnv
TCSC="0" NumberType="1" Negative="False" HasSpace="False" SourceValue="30"
UnitName="”" w:st="on">30”</st1:chmetcnv>should be 7-4 = 3, which is
significantly lower than the value (10) obtained in hbnum.xvg.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>I don't
what's wrong.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>Thanks <o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=3 face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'>Hu Qiu<o:p></o:p></span></font></p>
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