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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Thu, 28 Feb 2008 16:12:32 +0100<br>> From: lastexile7gr@yahoo.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] nrexcl 3 or 4 in combination with pairs 1-4<br>> <br>> Dear Gromacs users,<br>> <br>> my system has both 1-4 and 1-5 interactions. I list<br>> all of them in pairs. According to nrexcl definition<br>> (gmx mail list), "setting nrexcl to 3 or 4 does NOT<br>> remove LJ-14". Yet, by switching this option from 3 to<br>> 4 I have a lot of differences not only in the non<br>> bonded but also in bonded interactions as well. <br>> Searching further the forums I came accross :<br>> Priority of [ pairs ] and nrexcl?, yet it is<br>> unanswered. <br>> <br>> Question1:<br>> If I have both pairs 1-4 and nrexcl 3 that means that<br>> atoms, three bonds away, have non-bonded AND LJ14<br>> interaction or ONLY LJ14 interaction?<br><br>The naming in Gromacs is a bit confusing.<br>nrexcl excludes the normal LJ and Coulomb interactions.<br>LJ-14 refers to the interactions in the pairs, which are in biomolecular<br>force fields only used for 1-4 interactions.<br>I guess you would want to set nrexcl=4<br><br>> <br>> Question2:<br>> In pairs should I declare the atom indexes only once?<br>> For example i j is is enough for declaring the 1-4<br>> interaction between i and j or have I to insert also j<br>> i? Doing so I get different results.<br><br>Indeed.<br>You just define a pair interaction between atoms i and j.<br>Adding j-i adds another pair interaction between j and i, which,<br>since pair interactions are symmetric, is the same adding i-j.<br>Doubly defined bonded interactions lead to double bonded interactions.<br><br>Berk.<br><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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