Hi Mark,<br><br>I don't quite understand what it follows "only one [defaults] section can exist in an entire topology".<br><br>Then how to specify different fudge values for different subsets of non-bonded interactions?<br>
<br>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?<br>
<br>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?<br>
<br>Thanks,<br>Yun<br><br>Date: Sun, 18 Sep 2011 09:25:38 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] different sets of fudgeQQ and fudgeLJ<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E752C72.4040807@anu.edu.au">4E752C72.4040807@anu.edu.au</a>><br>
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<br>
On 18/09/2011 8:58 AM, Yun Shi wrote:<br>
> Hi all,<br>
><br>
> I want to apply different values of LJ and QQ scaling factors for two<br>
> interacting molecules A and B. Since I already have the .itp files for<br>
> each molecule, should I just add something like:<br>
><br>
> [ defaults ]<br>
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
> 1 2 yes 0.5<br>
> 0.8333<br>
><br>
> at the very beginning of A.itp and B.itp respectively (the actual<br>
> values are different from this eg.)?<br>
><br>
> I wonder if .itp file format was designed for this kind of purpose?<br>
> :) I guess we could even define different sets of atom types for A<br>
> and B, right?<br>
<br>
As you will see in the examples in chapter 5, only one [defaults]<br>
section can exist in an entire topology. Further, the fudge values only<br>
apply to a subset of non-bonded interactions. For the kind of<br>
calculation you have in mind, you will need to define new atom types for<br>
the modified interactions.<br>
<br>
Mark