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Dear Nancy,<br><br>
write it with a text editor.<br><br>
the file 'pair.ndx' could be this way (without the '----..-') :<br>
-------------------------------------
<dl>
<dd><tt>[ atom0 ]
<dd> 1<br>
<dd>[ atom1 ]
<dd> 21</tt>
</dl>-------------------------------------<br>
757 and 907 are the atom number, pick them from the *.gro
file <br><br>
Example: my *gro has this two atoms (1 and 21)<br>
-------------------------------------<br>
<tt> 1SER
N 1 2.304 3.357
-2.080<br>
...<br>
2GLN C
21 2.356 3.455 -1.605<br>
</tt>-------------------------------------<br><br>
<br>
the file 'pair.dat' could be this way (without the '----..-'):<br>
-------------------------------------<br>
<tt><x-tab> </x-tab>0
1<br>
</tt>-------------------------------------<br><br>
<br>
then issue: <br><br>
<tt><x-tab> </x-tab>g_dist
-f md.trr -s md.tpr -n pair.ndx -o dist_pair_t.xvg < pair.dat<br><br>
</tt>of course, put trajectory and tpr file in local dir.<br><br>
Diego Vallejo<br>
(BTW, nice pic)<br>
-------------------------------------------------------------<br><br>
<br>
Dear All,<br><br>
Would anyone mind telling me how to define the index of two atoms in
order<br>
to monitor the time-dependent distance between the pair??? For example,
the<br>
first atom is backbone "N" from residue 19, and the 2nd atom is
from<br>
sidechain "OD1" from residue 99.<br><br>
<br>
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