<DIV> Dear all,</DIV>
<DIV> </DIV>
<DIV>there is an error as follows:</DIV>
<DIV>---------------------------------------------------------<BR>Group 0 ( Nitrogen) has 2 elements<BR>There is one group in the index<BR>Will gather information on 1 bonds<BR>Last frame 2000 time 7000.000</DIV>
<DIV>Total number of samples : 2001<BR>Mean : 1.10008<BR>Standard deviation of the distribution: 0.0655399<BR>Standard deviation of the mean : 0.00146515</DIV>
<DIV>Back Off! I just backed up dNN.xvg to ./#dNN.xvg.1#<BR>Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !<BR>--------------------------------------</DIV>
<DIV>i 'd like to investigate distance between Nitrogen atom.</DIV>
<DIV>This is the command that i used:</DIV>
<DIV> g_bond -f md7.xtc -n index.ndx -s md7.tpr -o dNN.xvg -l dNN.log -d dNN.xvg<BR></DIV>
<DIV>And This is my index file:</DIV>
<DIV> </DIV>
<DIV>[ Nitrogen ]<BR>129 597<BR></DIV>
<DIV>PLease suggest me, what' s wrong?</DIV>
<DIV> </DIV>
<DIV>Best regards,</DIV>
<DIV>Chiloo<BR><B><I>leafyoung81-group@yahoo.com</I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">--- chiloo Laohpongspaisan <CHILOO77@YAHOO.COM>wrote:<BR><BR>> Dear All,<BR>> <BR>> If i'd like to investigate the distance between 2<BR>> atoms of the system (protein/bilayer/water), is the<BR>> command "g_bond"? And are there any options that<BR>> must be added to focus only two atoms.<BR>Yes. put two atoms into one group of the index file<BR>and specify the index file (with -n) for g_bond<BR><BR>> And If i'd like to investigate the movement of one<BR>> water molecule, how is the command?<BR>similarly, put the water molecule into one group of<BR>the index file and specify the index file (with -n)<BR>for g_trjconv to get the trajectory.<BR>> <BR>> Best regards,<BR>> chiloo<BR>> <BR>> <BR>> <BR>> <BR>> __________________________________________________<BR>> Do You Yahoo!?<BR>> Tired of spam? Yahoo! Mail has the best spam<BR>>
protection around <BR>> http://mail.yahoo.com ><BR>_______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please don't post (un)subscribe requests to the<BR>> list. Use the <BR>> www interface or send it to<BR>gmx-users-request@gromacs.org.<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR></BLOCKQUOTE><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com