Yun Shi wrote:
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?
The values of fudgeLJ and fudgeQQ are applied to intramolecular 1-4
interactions, thus they can only be present once in an entire topology. They
are global settings. If you wish to define different 1-4 interactions, then
define special [pairs], and if you want to use non-default nonbonded
interactions, then define them in [nonbond_params]. The latter sounds like what
you want, since it sounds like you want modified intermolecular interactions.
-Justin
Thanks,
Yun
Date: Sun, 18 Sep 2011 09:25:38 +1000
From: Mark Abraham <mark.abra...@anu.edu.au
<mailto: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
<mailto:gmx-users@gromacs.org>>
Message-ID: <4e752c72.4040...@anu.edu.au
<mailto: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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
