[gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 73

[Esra kaçar]

Dear Joe,

Thank you for your response. I have already read the selection syntax. In
my situation I do not want to select just one point which represents the
com or cog of the micelle. Sorry, may be I am not clear enough. My purpuse
is to calculate RDF as if calculating it around an axes. The problem here,
my axes is the backbone of the wormlike micelle and it is not straight. Is
there any way to do it with gromacs tools?
Many thanks,

Esra

Esra TUNÇER,

Research Assistant, Ph.D.c
Izmir Institute of Technology
Engineering Faculty
Department of Food Engineering
35430 Gulbahce-Urla, Izmir/Turkey
Phone: +90(232)7506285 <%2B90%28232%297506296>
Fax : +90(232)7506196
e-mail: esrakacar at iyte.edu.tr

2018-03-14 14:00 GMT+03:00 <
gromacs.org_gmx-users-request at maillist.sys.kth.se>:

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>    1. rdf calculation for wormlike micelles (Esra Ka?ar)
>    2. Re: rdf calculation for wormlike micelles (Joe Jordan)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Mar 2018 12:01:25 +0300
> From: Esra Ka?ar <esrakacar at iyte.edu.tr>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] rdf calculation for wormlike micelles
> Message-ID:
>         <CAArOx8LEN2HpGQA3xqQryeQZsDYcn4MZ83QWPje8qNZmCStxjA at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
>
> I am working on a wormlike micelle that has a curved structure. I want to
> calculate the radial distribution functions of constituent molecules with
> respect to the backbone (the line following the micelle length and
> represents the center of the curved cylindrical structure) of the wormlike
> micelle. Since the structure is curved, I couldn?t find out how to select
> the backbone as a reference point in g_rdf. I am using Gromacs v 5.1.  Any
> suggestions would be appreciated.
>
> Thanks,
>
> Esra
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 14 Mar 2018 10:12:42 +0100
> From: Joe Jordan <e.jjordan12 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] rdf calculation for wormlike micelles
> Message-ID:
>         <CAN-nNVNAVxMTjiAQcruLMvb7g+w_En8twmfi3oY3eqYEtCXyjQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> See here for info on the selection syntax
> http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
>
> On Wed, Mar 14, 2018 at 10:01 AM, Esra Ka?ar <esrakacar at iyte.edu.tr>
> wrote:
>
> > Dear all,
> >
> > I am working on a wormlike micelle that has a curved structure. I want to
> > calculate the radial distribution functions of constituent molecules with
> > respect to the backbone (the line following the micelle length and
> > represents the center of the curved cylindrical structure) of the
> wormlike
> > micelle. Since the structure is curved, I couldn?t find out how to select
> > the backbone as a reference point in g_rdf. I am using Gromacs v 5.1.
> Any
> > suggestions would be appreciated.
> >
> > Thanks,
> >
> > Esra
> > --
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>
> --
> Joe Jordan
>
>
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> End of gromacs.org_gmx-users Digest, Vol 167, Issue 73
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