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<DIV><FONT face=Arial size=2>Hi Deigo,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thank you so much for the very clear instruction. I
highly appreciate for all the details, and It works perfect now.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Do you have any clue to define the dihedral angle
among any four specified atoms??? If possible, I am thinking to measure the
angle between two nearby helix in terms of the customized
"dihedrals"....</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>nancy</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=diegovallejo@mdq.com.ar href="mailto:diegovallejo@mdq.com.ar">diego
vallejo</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, May 04, 2005 7:13
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] index
definition</DIV>
<DIV><BR></DIV>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>
</DD></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>
<P>
<HR>
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29/04/2005<BR>
<P>
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