My neighborlist is set to be updated every 10 steps. It core dumped in the 4th loop (outloop index n=4). From the printed-outs, in the first 3 loops, the neighborlists seem to be stable.<br><br>
<div><span class="gmail_quote">On 9/23/06, <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, Erik and other developers,<br>><br>> You might remember I posted several questions related to the C codes
<br>> (nb_kernelxyz) weeks ago.<br>> I've been trying to make a z-dependent only LJ interaction.<br>> Once I make rsq=dz*dz (instead of rsq=dx*dx+dy*dy+dz*dz), after a<br>> certain number of loops and steps, the coordinates of one neighbor
<br>> atom get quite large (of the order of 10^5), making rsq even larger.<br>> As r is then used to computer the index of VFtab, nnn, this leads to a<br>> nnn of the order of 10^9 and of course, the program cannot reach the
<br>> memory address of VFtab[1000000000]. So it goes to a segmentation fault.<br>><br>> I really don't understand why a small change in rsq (my system is a<br>> 128 DPPC with water, total 4700 coarse-grained atoms, dx dy is usually
<br>> around 1 nm for each step as printed out) will result in a sudden bump<br>> of pos[] (or rvec x[]) values. If you could shine some light on this<br>> issue, it will be very helpful.<br>><br>> I appreciate your responses!
<br>><br>> Chenyue Xing<br>How about your neighborlist? Is that updated as it should?<br><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
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