<div>Yeah. I printed r^2 out as well as all Zs. r^2 is really calculated based on Z.</div>
<div>So there's a r^2 calculation in neighborsearching too and it's somehow used in table look-up?<br><br> </div>
<div><span class="gmail_quote">On 10/18/06, <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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Chenyue Xing wrote:<br>> Hi Anton,<br>><br>> Thanks for the nice suggestions.<br>> As for the first possibility, I've been investigating and printed out
<br>> all the zi, zj, but haven't got a clue yet.<br>> As for the 2nd, the modified code still works in the same manner, that<br>> rsq = z^2 and then take the sqrt, so a negative r should not be a problem.<br>>
<br><br><br>have you checked r2 as well? I'm pretty sure it is the nieghboursearching.<br><br>> If you have any other guess, please let me know. That will help a lot.<br>><br>> Thank you !<br>> Chenyue<br>>
<br>><br>> On 10/18/06, *Anton Feenstra* <<a href="mailto:feenstra@few.vu.nl">feenstra@few.vu.nl</a><br>> <mailto:<a href="mailto:feenstra@few.vu.nl">feenstra@few.vu.nl</a>>> wrote:<br>><br>> Chenyue Xing wrote:
<br>> [...]<br>> > Thank you for your discussion and I hope I can provide more info<br>> soon so<br>> > that you might be able to give me more advices.<br>><br>> There are two problems I can think of that may be bothering you.
<br>> First is related to what David already mentioned: if you have an LJ-type<br>> interaction and your z becomes very small, the resulting force is HUGE.<br>> This can happen suddenly in your case when a particle enters the cutoff
<br>> (as determined by the neighbourlist update), with relatively large x or<br>> y, but small z.<br>> Second is that r=z is not really equivalent to the 3D case, because<br>> your<br>> r can become negative (I haven't looked at the code, but I suspect
<br>> something like z=zi-zj for particle i and j). In the 3D case, you have<br>> the squares and square-root. I can imagine that a negative r will not be<br>> present in the lookup table ;-)<br>><br>
><br>> --<br>> Groetjes,<br>><br>> Anton<br>><br>> _____________ _______________________________________________________<br>> | | |
<br>> | _ _ ___,| K. Anton Feenstra |<br>> | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |<br>> |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |
<br>> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |<br>> | | <a href="mailto:Feenstra@few.vu.nl">Feenstra@few.vu.nl</a> <mailto:<a href="mailto:Feenstra@few.vu.nl">Feenstra@few.vu.nl
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