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Hi,<br><br>I don't understand your mail.<br>Do you really get a segmentation fault, but also frames in your trajectory file?<br><br>I think I fixed the freezing of the whole system bug.<br>I tested it for a water system and it runs fine.<br><br>Maybe you have constraints in your system.<br>Asking your system to be completely frozen and to obey the constraints<br>is usually contradictory. Therefore you system might still move slightly<br>to try to obey the constraints.<br><br>Anyhow it seems pretty useless to me to simulate a completely frozen system.<br><br>Berk<br><br>> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> Date: Mon, 10 Nov 2008 15:13:06 +0100<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] freeze group gives Segmentation fault<br>> <br>> <br>> I just tried Gromacs 4.0.2. It still gives a Segmentation fault:<br>> <br>> "Reading file topol.tpr, VERSION 4.0.2 (single precision)<br>> Loaded with Money<br>> <br>> Segmentation fault"<br>> <br>> I did a test, putting the whole system into one freezegroup. Then the <br>> simulation starts running. But some of the atoms belonging to the <br>> "freeze-group" still move: The RMSD keeps growing and the Potential <br>> Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the <br>> molecules moving. There is no pattern in the motion though. I checked <br>> the index.ndx twice - there is no mistake in there.<br>> <br>> Ilona<br>> <br>> <br>> > There was a bug in the freeze group code that got fixed today. I <br>> > don't know anything else about it. Please update your source code <br>> > and try again.<br>> ><br>> > Mark<br>> <br>> <br>> > ilona.baldus@bioquant.uni-heidelberg.de wrote:<br>> >><br>> >> Using freezegroups I get a Segmentation fault. The simulation does <br>> >> not start, so the output is empty.<br>> >><br>> >> "Reading file topol.tpr, VERSION 4.0_rc4 (single precision)<br>> >> Segmentation fault"<br>> <br>> <br>> <br>> <br>> <br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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