<div>Hi David,</div>
<div> </div>
<div>Thank you for your quick reply.</div>
<div>I tried setenv and compared 2 simulations with exactly the same initial structure and parameters (one w/ NOASSEMBLYLOOPS, one w/o it)</div>
<div>But the results seem to be different. Is this normal?</div>
<div> </div>
<div>Here's my data:</div>
<div>initial structure:</div>
<div>Testing 3 particles (particle 2W,3W are positionally fixed) <br> 3<br> 1W W 1 3.237 3.574 3.584 0.0000 0.0000 0.5000<br> 2W W 2 3.637 3.574 5.000 0.0000 0.0000 0.0000<br>
3W W 3 2.637 3.574 0.000 0.0000 0.0000 0.0000<br> 6.00000 6.00000 6.00000<br> </div>
<div>w/o NOASSEMBLYLOOPS final structure<br>testing 3 particles<br> 3<br> 1W W 1 5.109 3.574 4.720 0.0690 0.0000 0.3215<br> 2W W 2 3.637 3.574 5.000 0.0000 0.0000 0.0000<br>
3W W 3 2.637 3.574 0.000 0.0000 0.0000 0.0000<br> 6.00000 6.00000 6.00000<br> </div>
<div>w/ setenv NOASSEMBLYLOOPS 1 final structure</div>
<div>testing 3 particles<br> 3<br> 1W W 1 5.561 3.574 2.893 -0.2213 0.0000 -0.2213<br> 2W W 2 3.637 3.574 5.000 0.0000 0.0000 0.0000<br> 3W W 3 2.637 3.574
0.000 0.0000 0.0000 0.0000<br> 6.00000 6.00000 6.00000<br>(I assume w/ NOASSEMBLYLOOPS 1, it runs w/ c codes?)</div>
<div><br> </div>
<div>Also, if I have assemblyloops enabled (not setting noassemblyloops 1), can I actually find those assembly codes to read?</div>
<div> </div>
<div>Thank you very much again!</div>
<div> </div>
<div> </div>
<div><span class="gmail_quote">On 9/2/06, <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 all,<br>><br>> I'm trying to make the nonbonded interaction between 2 particles (let's
<br>> say 2 water particles for now) z-dependent only. So I went into the<br>> innerloop code (v3.3.1) to change rsq to "rsq = dz*dz". I changed this<br>> in mknb_innerloop.c so that it automatically updates all the nb_kernel
<br>> files when being compiled. However, this doesn't seem to have different<br>> results from the original r-dependent interation. (meaning, with the<br>> same initial conditions, the systems ended up in the same final conditions)
<br>><br>> That sounds like not nb_kernelxxx_c.c codes are being used when doing<br>> simulations.<br>> Can any expert help me with this issue?<br>> If it's sth related Gromacs compiled w/ assembly compiler, how can
<br>> disable asm for now? (guess I won't anyway be able to change any ASM<br>> related stuff)<br><br>setenv NOASSEMBLYLOOPS 1<br>><br>> Thanks a lot!!<br>><br>> -Chenyue<br>><br>><br>> ------------------------------------------------------------------------
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</a>.<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<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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