[gmx-users] RDF calculation

2018-05-02 Thread Esra kaçar 
Dear all,

I have a curved rod-like micelle formed by three different molecules. I
want to calculate the RDF of constituent molecules. I want to select the
center line of the curved cylindir-like structure as a reference point. How
can I do that? I am using Gromacs version 5.1.2. with Martini Force field.
Any suggestions would be helpful.

Many thanks,

Esra
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Re: [gmx-users] rdf calculation for wormlike micelles

2018-03-16 Thread Esra kaçar 
Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

Esra


2018-03-14 17:51 GMT+03:00 :

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>2. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Joe Jordan)
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> From: Esra ka?ar 
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> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue
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Re: [gmx-users] rdf calculation for wormlike micelles

2018-03-15 Thread Esra Kaçar 
Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

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

2018-03-14 Thread 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: esraka...@iyte.edu.tr

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

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> Today's Topics:
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>1. rdf calculation for wormlike micelles (Esra Ka?ar)
>2. Re: rdf calculation for wormlike micelles (Joe Jordan)
>
>
> --
>
> Message: 1
> Date: Wed, 14 Mar 2018 12:01:25 +0300
> From: Esra Ka?ar 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] rdf calculation for wormlike micelles
> Message-ID:
>  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 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] rdf calculation for wormlike micelles
> Message-ID:
>  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 
> 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
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> Joe Jordan
>
>
> --
>
> --
> Gromacs Users mailing list
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> End of gromacs.org_gmx-users Digest, Vol 167, Issue 73
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[gmx-users] rdf calculation for wormlike micelles

2018-03-14 Thread Esra Kaçar 
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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[gmx-users] improper .gro file format generated by trjconv

2016-05-16 Thread Esra Kaçar 
Dear gromacs users;

I am trying to perform micelle clustering analysis as described in gromcas
website:

   1. use trjconv
    -pbc
   cluster to obtain a single frame that has all of the lipids in the unit
   cell. This must be the first frame of your trajectory. A similar frame from
   some previous timepoint will not work.
   2. use grompp
    to make
   a new tpr file based on the frame that was output from the step above.
   3. use trjconv
    -pbc
   nojump to produce the desired trajectory using the newly produced tpr
   file.

Firstly I am trying to use trjconv to have a .gro file, but the output of
first step gives me a .gro file in improper format, i.e.coordinates are not
written with required spaces between each other. Here is my command line:

gmx trjconv -f mytrajectory.xtc -o micelle.gro -s mytopology.tpr -e 0.001
-pbc cluster

And here is the micelle.gro file:

1CHOA   ROH1   2.7   8.2   7.7
1CHOA  R12   3.0   8.1   7.7
1CHOA  R23   3.2   8.1   7.8
1CHOA   RO24   3.2   7.8   7.7
1CHOA   RO35   3.4   7.8   7.9
1CHOA  R36   3.4   7.8   7.7
1CHOA  C17   3.6   7.5   7.7
1CHOA   OCO8   3.5   7.1   7.6

What can be the possible reason for this error and how can I fix it?

With regards,
Esra
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