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<br><br>> Date: Fri, 16 Jan 2009 09:06:43 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Inconsistent shifts Problem when using g_rdf<br>> <br>> Lin, Pohan wrote:<br>> > I am running NPT simulations by using Parrinello-Rahman pressure <br>> > coupling on Gromacs 3.3.3. My system contains epoxy and cross-linker <br>> > molecules. By modifying the topology file (add bond, angle, torsion <br>> > terms in topology), all the molecules are connected together to be an <br>> > huge polymeric molecule. The MD jobs were running well before and after <br>> > polymerization. However, while analyzing the data by using g_rdf, it <br>> > keeps showing the message “There were XXX inconsistent shifts. Check <br>> > your topology” for the structures after polymerization and the g(r) are <br>> > not reasonable. Does anyone have any idea about this issue? I am also <br>> > curious about how g_rdf deal with “inconsistent shifts.” Does g_rdf <br>> > ignore those data or do something else?<br>> <br>> Probably, yes. I think it will go fine in version 4.0 though. Please <br>> wait until 4.0.3 before upgrading.<br><br>Many analysis tools will give these inconsistent shift errors when you<br>have periodic molecules in the system.<br>This has not changed in version 4.0.<br><br>g_rdf only uses requires the shifting for removing pairs that are excluded<br>through bonded interactions.<br>If you do not encounter such pairs in your analysis, or you don't care about<br>the peaks they will cause at short distance, you can supply only an<br>index file to g_rdf and no tpr file. In that case the shift code will not be used.<br><br>Berk<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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