<div>I actually tested my new interaction on a 3-atom system and it worked fine.</div>
<div>Then I moved on to this complicated system.</div>
<div>It looks like the system takes quite a bit steps to get out of control.</div>
<div>Do you think rsq=dx*dx+dy*dy+dz*dz and rsq=dz*dz will have a very big difference? As r will be used as r^6 and r^12 (r^7 and r^13 for force), I assume the <1 value difference will have even smaller influence on the energy and force part.
</div>
<div> </div>
<div>I really appreciate your help and hopefully you could point out my mistake somewhere.</div>
<div> </div>
<div>Thanks,</div>
<div>Chenyue <br><br> </div>
<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>> My neighborlist is set to be updated every 10 steps. It core dumped in<br>> the 4th loop (outloop index n=4). From the printed-outs, in the first
<br>> 3 loops, the neighborlists seem to be stable.<br><br>if your atoms fly away there is something wrong :)<br>are you sure your forces are correct?<br>you should test the algorithm on a simple system and check for energy
<br>conservation.<br><br>><br>> On 9/23/06, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:
<br>><br>> Chenyue Xing wrote:<br>> > Hi David, Erik and other developers,<br>> ><br>> > You might remember I posted several questions related to the C<br>> 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<br>> leads to a<br>> > nnn of the order of 10^9 and of course, the program cannot reach
<br>> the<br>> > memory address of VFtab[1000000000]. So it goes to a<br>> 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<br>> usually<br>> > around 1 nm for each step as printed out) will result in a<br>> 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?
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