<div>Hi David,</div>
<div> </div>
<div>I actually tried with a 3-atom system first and that worked perfect. Then I tried a larger system which now has the segfault problem. My conformation is good at least for normal interactions and the fz only case. Maybe there's some conflict or inconsistency when I do a r=z case?
</div>
<div>As the huge r first appeared in the 4th step (I suspected there's inequilibrium in the system), I used a more frequent nblist update to see if it can avoid that but no luck. And a nblist_update freq=1 gives stuck (infinite loop somewhere maybe?). So would you come across any guess that I might unfortunately do anything bad with the neighborlist codes (I haven't modified the neighborlist codes though).
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<div> </div>
<div>Thank you very much!</div>
<div>Chenyue<br><br> </div>
<div><span class="gmail_quote">On 10/17/06, <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 David,<br>><br>> I want to use just a LJ potential for a z-dependent only interaction. I
<br>> noticed that 1/r^n and 1/r^(n+1) are used for energy and force<br>> calculation so I tried to set r = z only.<br>><br>> Hope you can give me more advices.<br>> Thank you very much!<br>><br>><br>
<br>I don't see why it shouldn't work, except when your starting<br>conformation is bad (or a programming error of course). Try with a two<br>particle test system first.<br><br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
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