Hi Mark, I don't quite understand what it follows "only one [defaults] section can exist in an entire topology".
Then how to specify different fudge values for different subsets of non-bonded interactions? When defining new atom types, should I always use 'new' atomtypes names? For example, if the atom type "H2" already exists for part A, then I should use something different like "H2B" to define similar atomtypes in part B? But if I can use only one [ defaults ] section, even within different .itp files under the same .top file, how could I tell the program to apply different fudge values to H2 as defined in A.itp and H2B as defined in B.itp? Thanks, Yun Date: Sun, 18 Sep 2011 09:25:38 +1000 From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] different sets of fudgeQQ and fudgeLJ To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4e752c72.4040...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 18/09/2011 8:58 AM, Yun Shi wrote: > Hi all, > > I want to apply different values of LJ and QQ scaling factors for two > interacting molecules A and B. Since I already have the .itp files for > each molecule, should I just add something like: > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 > 0.8333 > > at the very beginning of A.itp and B.itp respectively (the actual > values are different from this eg.)? > > I wonder if .itp file format was designed for this kind of purpose? > :) I guess we could even define different sets of atom types for A > and B, right? As you will see in the examples in chapter 5, only one [defaults] section can exist in an entire topology. Further, the fudge values only apply to a subset of non-bonded interactions. For the kind of calculation you have in mind, you will need to define new atom types for the modified interactions. Mark
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