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<br><br>> Date: Mon, 10 Aug 2009 20:52:31 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups<br>> <br>> Lee Soin wrote:<br>> > 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>> <br>> Since there is no bonded interaction between 1 and 4, your second [ <br>> exclusions ] directive will not have any effect. Read section 5.4. <br>> Exclusions are cancellations only of interactions between bonded atoms.<br>> <br><br>That is incorrect.<br>The exclusion line makes Gromacs excluded non-bonded interactions<br>between atoms 1 and 4. The [ exclusions ] section, although itself<br>"bonded" in some ways, has no relation at all with any other bonded<br>interactions.<br><br>Berk<br><br>> > 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>> <br>> mdrun is only reproducible if you tell it that you want it to be with <br>> "mdrun -reprod". So it is possible that your observation of different <br>> results is not (yet) meaningful.<br>> <br>> However, I believe you've merely added a second identical non-bonded <br>> interaction between 1 and 4, so you will get different results regardless.<br>> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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