Amber mdcrd trajectory has the same format of .g87 (title, x(i) and box). <br>
I tried g_hbond -e 750 but it gave me the same. I notice
that in the manual, you have .g96 instead .g87 mostly. Is it because
.g87 can not be read and analyzed any more? Thank you for your
help and information. <br>
<br>
sincerely<br>
Lydia<br><div><span class="gmail_quote">On 2/18/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Lydia wrote:<br>> If I calculate hbond it won't give error information but the<br><br>try g_hbond -e 750<br>to see whether the beginning of the traj is OK.<br><br>If the format is not as expected I don't know how to fix it. Maybe you
<br>can mould our trajecotry into another format using some kind of script.<br>Otherwise just try and rerun the simulation...<br><br>> hbnum.xvg will be<br>> -----------------------------------------------------------------------------------------------------------------
<br>> cat hbnum.xvg<br>><br>> # This file was created Sat Feb 18 08:44:34 2006<br>> # by the following command:<br>> # g_hbond -f nmwt.g87 -s nmwt.tpr -n index.ndx -num -hbm -a 120<br>> #<br>> # g_hbond is part of G R O M A C S:
<br>> #<br>> # GRowing Old MAkes el Chrono Sweat<br>> #<br>> @ title "Hydrogen Bonds"<br>> @ xaxis label "Time"<br>> @ yaxis label "Number"<br>> @TYPE xy<br>> @ view
0.15, 0.15, 0.75, 0.85<br>> @ legend on<br>> @ legend box on<br>> @ legend loctype view<br>> @ legend 0.78, 0.8<br>> @ legend length 2<br>> @ s0 legend "Hydrogen bonds"<br>> @ s1 legend "Pairs within
0.35 nm"<br>> 801 11
4<br>> ----------------------------------------------------------------------------------------------------------------<br>> I'm expecting 800 rows of numbers which are the number of hbonds<br>> as a function of time (800ps). But it has only one row to give out
<br>> the average number of hbonds per timeframe 11.000 out of 330 possible.<br>><br>> Best wishes<br>> Lydia<br>><br>><br>> ------------------------------------------------------------------------<br>
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<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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