Hi David,<br><br>Thank you for your suggestion!<br><br>But I heard that there's some bugs to make hole with the later versions (is it true?), so I choosed 3.1.4 to make hole.<br>I also installed 3.2.1, so I inserted the protein to the bilayer with a hole, generated with
3.1.4. Then I tried to minimize this system with 3.2.1, I got the following error messages when I did mdrun:<br><br>Warning: 1-4 interaction between 41 and 51 at distance larger than 2 nm<br>These are ignored for the rest of the simulation
<br>turn on -debug for more information<br>Fatal error: ci = -2147483648 should be in 0 .. 2365 [FILE nsgrid.c, LINE 218]<br><br>Could you tell me what to do with it?<br><br>Thanks in advance!<br><br><div><span class="gmail_quote">
On 12/8/05, <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;">
liu xin wrote:<br>> Dear gmx-users;<br>><br>> When I tried to minimize my lipid/protein system I got a "segmetation<br>> fault" error message and the mdrun program stopped, then I checked the<br>>
em.log file found there was a warning "There were 2 inconsistent shifts.<br>> Check your topology". Did this warning cause the stop?.<br>><br>> I searched this forum and did as told before: to add a line "pbc = xyz"
<br>> to my em.mdp, and export GMXFULLPBC = 1. But I still got this two<br>> messages. I started the mdrun like $/home/xin/program/.../mdrun, and I<br>> export like $export GMXFULLPBC, did I do it in a wrong way? My system is
<br>> SUSE 9.0, GMX 3.1.4, I am new to GMX and Linux, could anybody so kind<br>> tell me how to over come this problem?<br>please upgrade gromacs<br>><br>> Thanks in advance!<br>><br>> Liu Xin<br>><br>
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<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
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