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<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Is it possible to add connectivity information in the
trajectory file? I’m dealing with CG MD using Martini FF.
After the production run, I checked my trajectory by loading the full.gro and
full.trr in VMD. However, I could see nothing but a stack of CG beads moving
around. No bonds there. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>It was mentioned that (maybe in the revision history,
I couldn’t find it any more as gromacs is moving to a new site) Gromacs <st1:chsdate
IsROCDate="False" IsLunarDate="False" Day="30" Month="12" Year="1899" w:st="on">4.0.5</st1:chsdate>
is able to add connectivity information in the trajectory file, which is very
helpful in CG simulation. I got one trajectory file in pdb format by
trying the following command:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Trjconv –f full.trr –s full.tpr –n
index.ndx –o test.pdb<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>I checked the test.pdb(with many frames) and found no
connectivity information. How could I add connectivity information in the
trajectory file? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Any suggestions are greatly appreciated!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Many thanks in advance!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Yours, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Chuan Liao<o:p></o:p></span></font></p>
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