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Hi David,
<br>Thanks a lot for your reply,
<br>The starting coordinates comes from EM, and they look like OK. If the
topology is bad, how can I check where is exactly the error?
<br>Thanks again
<br>cheers,
<br>Ruben
<p>David van der Spoel wrote:
<blockquote TYPE=CITE>On Fri, 2003-01-10 at 20:01, Ruben Martinez Buey
wrote:
<br>> Hi all,
<br>> I´m testing the gromacs molecular topology of a small molecule generated
<br>> by PRODRG using GROMACS EM/MD. EM runs OK but MD stops just after
start:
<br>>
<br>> Warning: 1-4 interaction at distance larger than 2.25
<br>> These are ignored for the rest of the simulation
<br>> turn on -debug for more information
<br>> Bus error (core dumped)
<br>>
<br>> How can I correct this?
<br>It's either the topology or the starting coordinates. Could it be a
<br>periodic boundary problem? (i.e. molecule split in two bits?)
<p>>
<br>> Thanks in advance for your kind attention,
<br>> with best wishes,
<br>> Ruben
<br>>
<br>>
<br>>
<br>>
<br>>
<br>>
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<br>--
<br>Groeten, David.
<br>________________________________________________________________________
<br>Dr. David van der Spoel,
Biomedical center, Dept. of Biochemistry
<br>Husargatan 3, Box 576,
75123 Uppsala, Sweden
<br>phone: 46 18 471 4205
fax: 46 18 511 755
<br>spoel@xray.bmc.uu.se spoel@gromacs.org
<a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a>
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<pre>--
___________________________________________
Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144 28006 MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________</pre>
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