I'm checking. For box, is it 3*10 or 3*8 per frame?
I do see difference in the defined format between .g87 and amber for
the box as the following: <br>
For .g87: <br>
<pre>--------------------------------------------------------------------------<br>TITLE<br>x(i) (10f8.3)<br>box(m) (10f8.8)<br>----------------------------------------------------------------------------</pre>
<br>
For amber: <br>
---------------------------------------------------------------------------------------<br>
<a name="trajectory">
<h3>AMBER trajectory (coordinate or velocity) file specification
</h3>
</a>
This file is optionally written during dynamics in
<tt>SANDER</tt> or <tt>GIBBS</tt>.
<pre>FORMAT(20A4) ITITL<br> ITITL : the title of the current run, from the AMBER<br> parameter/topology file<br></pre>
The following snapshot is written every <tt>NTWX</tt> steps in the
trajectory (specified in the control input file):
<pre>FORMAT(10F8.3) (X(i), Y(i), Z(i), i=1,NATOM)<br> X,Y,Z : coordinates or velocities (velocity units: Angstroms per 1/20.455 ps)<br></pre>
<h4>IF constant pressure (in 4.1, also constant volume)</h4>
For each snapshot:
<pre>FORMAT(10F8.3) BOX(1), BOX(2), BOX(3)<br>--------------------------------------------------------------------------------------- <br><span style="font-family: arial,sans-serif;"><br><br></span><br></pre>
sincerely<br>
lydia<br><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>> I don't want to rerun because there are too many to rerun. But I<br>> still want to use gromacs analysis tool which is very powerful.<br><br>Then you'll have to debug a bit further. I suspect the file and the
<br>software go out of sync somewhere. Does it work to read 100 frames? 10<br>frames? 1 frame? (Use the -e option again).<br><br>You should be able to read 1 frame and compute hbonds on it.<br><br>Also you could try to check the file size. If you have Natom atoms then
<br>the file size should be Natom*3*8 bytes + 3*10 bytes (box) per frame,<br>plus 80 bytes for a title. Thus<br>Filesize = 80 + Nframe * ( Natom*3*8 + 3*10 )<br>It might be that an extra character is stored per line in the file
<br>(newline), this you could take into account by subtracting the number of<br>lines in the file (wc file.g87)<br><br>Good luck...<br><br>> Lydia<br>><br>> On 2/18/06, *Lydia* <<a href="mailto:aether2006@gmail.com">
aether2006@gmail.com</a> <mailto:<a href="mailto:aether2006@gmail.com">aether2006@gmail.com</a>>><br>> wrote:<br>><br>> Amber mdcrd trajectory has the same format of .g87 (title, x(i)<br>> and box).
<br>> I tried g_hbond -e 750 but it gave me the same. I notice that in<br>> the manual, you have .g96 instead .g87 mostly. Is it because .g87<br>> can not be read and analyzed any more? Thank you for your help and
<br>> information.<br>><br>> sincerely<br>> Lydia<br>><br>> On 2/18/06, *David van der Spoel* < <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> 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.<br>> Maybe you<br>> can mould our trajecotry into another format using some kind of<br>> script.<br>> Otherwise just try and rerun the simulation...
<br>><br>>> hbnum.xvg will be<br>>><br>> -----------------------------------------------------------------------------------------------------------------<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>> ----------------------------------------------------------------------------------------------------------------<br>>> I'm expecting 800 rows of numbers which are the number of<br>
> hbonds<br>>> as a function of time (800ps). But it has only one row to<br>> give out<br>>> the average number of hbonds per timeframe 11.000 out of 330<br>> possible.<br>
>><br>>> Best wishes<br>>> Lydia<br>>><br>>><br>>><br>> ------------------------------------------------------------------------<br>>><br>>> _______________________________________________
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</a><br>><br>><br>> --<br>> David.<br>> ________________________________________________________________________<br>><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
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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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