<div>Hi Anton,</div>
<div> </div>
<div>Thanks for the nice suggestions.</div>
<div>As for the first possibility, I've been investigating and printed out all the zi, zj, but haven't got a clue yet.</div>
<div>As for the 2nd, the modified code still works in the same manner, that rsq = z^2 and then take the sqrt, so a negative r should not be a problem.</div>
<div> </div>
<div>If you have any other guess, please let me know. That will help a lot.</div>
<div> </div>
<div>Thank you !</div>
<div>Chenyue<br><br> </div>
<div><span class="gmail_quote">On 10/18/06, <b class="gmail_sendername">Anton Feenstra</b> <<a href="mailto:feenstra@few.vu.nl">feenstra@few.vu.nl</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>[...]<br>> Thank you for your discussion and I hope I can provide more info 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 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> - <a href="http://www.few.vu.nl/~feenstra/">www.few.vu.nl/~feenstra/
</a> |<br>| | "If You See Me Getting High, Knock Me Down" (RHCP) |<br>|_____________|_______________________________________________________|<br>_______________________________________________
<br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-developers">http://www.gromacs.org/mailman/listinfo/gmx-developers
</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br>