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<br><br>> Date: Mon, 10 Aug 2009 22:11:57 +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>> Berk Hess wrote:<br>> > <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>> >> 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>> True, 5.4 does point out that there are (in a sense) two kinds of <br>> exclusions, viz "The exclusions for bonded particles are generated by <br>> grompp for neighboring atoms up to a certain number of bonds away, as <br>> defined in the [ moleculetype ] section in the topology file (see <br>> 5.7.1).". Then the second paragraph goes on to point out the purpose of <br>> [ exclusions ]: "Extra exclusions within a molecule can be added <br>> manually in a [ exclusions ] section."<br>> <br>> Perhaps the wording of this description could be improved, since the <br>> sense of "[ exclusions ]" is actually "[ extra_exclusions ]"? A sentence <br>> clarifying this before the full explanation would make things clearer:<br>> <br>> "Exclusions<br>> <br>> Additional pairs of particles from which non-bonded interactions are to <br>> be excluded may be indicated under this directive. Some exclusions for <br>> bonded particles may be generated by grompp for neighbouring atoms...<br>> <br>> Such extra exclusions within a molecule can be added manually in the [ <br>> exclusions ] list. Each line..."<br>> <br>> Mark<br>> <br><br>The phrase "The exclusions for bonded particles" is indeed confusing.<br>I now replaced it by:<br>The exclusions for non-bonded interactions are generated by grompp...<br><br>I also added a few more words in this section to clarify things.<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>> >> 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>> > _________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <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>> 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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