<br><br>
<div class="gmail_quote">2009/8/10 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
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<div class="h5">Lee Soin wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hello!<br>Sorry to bother you again, but I have another question. I have written a<br>topology file of two water molecules to test the pair interaction. Here is<br>
part of my topology file:<br><br>[ moleculetype ]<br>SOL 2<br>[ atoms ]<br> 1 opls_116 1 SOL OW 1 -0.82<br> 2 opls_117 1 SOL HW1 1 0.41<br> 3 opls_117 1 SOL HW2 1 0.41<br> 4 opls_116 2 SOL OW 2 -0.82<br>
5 opls_117 2 SOL HW1 2 0.41<br> 6 opls_117 2 SOL HW2 2 0.41<br>[ settles ]<br> 1 1 0.1 0.16330<br> 4 1 0.1 0.16330<br>[ exclusions ]<br> 1 2 3<br> 2 1 3<br> 3 1 2<br> 4 5 6<br> 5 4 6<br> 6 4 5<br>
[ exclusions ]<br>1 4<br>[ pairs ]<br> 1 4 1<br><br>I have also changed the fudgeLJ and fudgeQQ to 1.0.<br>Originally, there is no pair interaction in this system. First I did a<br>simulation when the last 4 lines were removed, that is, I treated all the<br>
interactions as non-bonded interactions. <br></blockquote><br></div></div>Since there is no bonded interaction between 1 and 4, your second [ exclusions ] directive will not have any effect. Read section 5.4. Exclusions are cancellations only of interactions between bonded atoms.
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Then I added the last 4 lines<br>to specify the normal non-bonded interaction between atom 1 and 4 as pair<br>
interaction in order to see whether that will affect the result. It turns<br>out that the results for the two cases are different. So did I miss<br>something, or are pair interactions and non-bonded interactions treated<br>
differently by GROMACS?<br></blockquote><br></div>mdrun is only reproducible if you tell it that you want it to be with "mdrun -reprod". So it is possible that your observation of different results is not (yet) meaningful.</blockquote>
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<div>Actually, I added the option "-reprod" and the results are reproducible. The results for the </div>
<div>above-mentioned two cases are always different. So I am very confused.</div>
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><span></span><br><br>However, I believe you've merely added a second identical non-bonded interaction between 1 and 4, so you will get different results regardless.</blockquote>
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<div>Then I tried to remove the two lines:<br>[ exclusions ]<br>1 4<br>And retained the pair interaction that I have defined. But this lead to no difference in the </div>
<div>simulation result. Is it that the "exclusion" of non-bonded interaction between atom 1 and </div>
<div>atom 4 didn't work?<br>On the other hand, in another set of simulations, I removed the pair interaction part:<br>[ pairs ]<br> 1 4 1<br>In this case, the presence and absence of the "exclusion" part do make a dramatic </div>
<div>difference.<br>So can this conclusion be drawn: the presence of a pair interaction automatically eliminates </div>
<div>the corresponding non-bonded interaction?</div>
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<div><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<div></div><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>