Thanks. I tried the g_rms command and it seemed no problem.<br>What I am working on is rubisco, a very big protein and it has small subunits. I think the subunits are not in big size. My work is to calculate the number of hydrogen bond between the subunits in different time interval of the simulation. There is problem(floating exception) only in one time interval.
<br>Thank you!<br><br><br><div><span class="gmail_quote">On 9/4/07, <b class="gmail_sendername">Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">Florian.Haberl@chemie.uni-erlangen.de</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;">Hi,<br><br>On Tuesday, 4. September 2007 09:49, TANG JIAOWEI wrote:<br>> Dear all,
<br>> I am beginner in Gromacs. When I used g_hbond to calculate the number<br>> of hydrogen bonds between two proteins, "floating exception" happened. I<br>> try it many times, and the same problem is still exsits. Could you tell me
<br>> what is the problem?<br>> Thank you !<br><br>Please specify your problem more<br><br>- size of the system, protein<br><br>does other utilities work, does g_hbond work with smaller systems on your<br>hardware?<br>
<br>g_hbond needs huge amount of memory, perhaps you have to change your index<br>groups to a smaller number our change your analysis computer.<br><br><br><br>><br>><br>> Jiaowei Tang<br><br><br>Greetings,<br><br>
Florian<br><br>--<br>-------------------------------------------------------------------------------<br> Florian Haberl<br> Computer-Chemie-Centrum<br> Universitaet Erlangen/ Nuernberg<br> Naegelsbachstr 25<br> D-91052 Erlangen
<br> Telephone: +49(0) − 9131 − 85 26581<br> Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">chemie.uni-erlangen.de</a><br>-------------------------------------------------------------------------------
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