[gmx-users] rdf calculation for wormlike micelles

Esra kaçar esra176 at gmail.com
Fri Mar 16 07:52:26 CET 2018 

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 <gromacs.org_gmx-users-request
@maillist.sys.kth.se>:

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> Today's Topics:
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>    1. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Esra ka?ar)
>    2. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Joe Jordan)
>    3. Umbrella Sampling - good histogram but no result in       profile
>       (Ben Tam)
>    4. Re: Umbrella Sampling - good histogram but no result in
>       profile (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Mar 2018 16:28:19 +0300
> From: Esra ka?ar <esra176 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue
>         73
> Message-ID:
>         <CAArOx8Js90ouyU4CRLB3w09e8OZXNcpwKVf_HA114duDyM0V=A at mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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 TUN?ER,
>
> 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>:
>
> > Send gromacs.org_gmx-users mailing list submissions to
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> x-users
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> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >    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 <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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
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> > > send a mail to gmx-users-request at gromacs.org.
> >
> >
> >
> >
> > --
> > Joe Jordan
> >
> >
> > ------------------------------
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 167, Issue 73
> > ******************************************************
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 14 Mar 2018 15:21:50 +0100
> From: Joe Jordan <e.jjordan12 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue
>         73
> Message-ID:
>         <CAN-nNVO4vQA0e=oziksieGxrd8y8jXQLjRO8wFUFSO_d3vUB1w at mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Does it not work to just use alpha carbons as the reference? If this is not
> what you mean, you may need to be more specific in your query.
>
> On Wed, Mar 14, 2018 at 2:28 PM, Esra ka?ar <esra176 at gmail.com> wrote:
>
> > 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
> >
> >
> > 2018-03-14 14:00 GMT+03:00 <
> > gromacs.org_gmx-users-request at maillist.sys.kth.se>:
> >
> > > Send gromacs.org_gmx-users mailing list submissions to
> > >         gromacs.org_gmx-users at maillist.sys.kth.se
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > >         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > gmx-users
> > > or, via email, send a message with subject or body 'help' to
> > >         gromacs.org_gmx-users-request at maillist.sys.kth.se
> > >
> > > You can reach the person managing the list at
> > >         gromacs.org_gmx-users-owner at maillist.sys.kth.se
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of gromacs.org_gmx-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    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 <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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > >
> > >
> > >
> > >
> > > --
> > > Joe Jordan
> > >
> > >
> > > ------------------------------
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > > End of gromacs.org_gmx-users Digest, Vol 167, Issue 73
> > > ******************************************************
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> > send a mail to gmx-users-request at gromacs.org.
>
>
>
>
> --
> Joe Jordan
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 14 Mar 2018 14:44:08 +0000
> From: Ben Tam <btam125 at hotmail.co.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] Umbrella Sampling - good histogram but no result
>         in      profile
> Message-ID:
>         <CWXP265MB0229DACE6BDDFB21C1A2B9B9BED10 at CWXP265MB0229.GBRP26
> 5.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
> I have a rather strange problem. Currently I am trying to get a PMF of a
> water molecule through a hydrophobic materials. At the end of using "gmx
> wham", I get a rather good histogram and it cover the whole range of the
> system. However at the making profile.xvg. I get the answer "nan" inside
> the file. Therefore I really cannot think of why is it giving me that?
>
> Currently I set it as :
> ;Pull code
> pull = yes
> ;pull-cylinder-r = 0.5
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = SOL
> pull_group2_name = MOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = direction-periodic ; simple distance increase,
> direction-periodic
> pull_coord1_vec = 1 1 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y Y Y
> pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10000 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> Also this appears when I used the command "gmx wham":
>
> Switched to exact iteration in iteration 1
>            1) Maximum change -1.000000e+20
> Converged in 2 iterations. Final maximum change -1e+20
>
> Therefore I really don't understand what I have to do in order to get a
> profile.xvg. I understand the k value is high, but without that high value,
> the water won't settle within the assign window.
>
> Am I doing something wrong? because I got a good histogram but no result
> in the profile.xvg? Thank you very much for your help.
>
> Best regards,
>
> Ben
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 14 Mar 2018 14:51:17 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no
>         result in       profile
> Message-ID:
>         <CAMNuMAROnzm0PtgnL4L+qNgntuL8zY6LqfF68G-AqdgTG1tS6g at mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> That would generally suggest something divided by zero, or similar, eg
> because no data was in a histogram bin, etc.
>
> That behavior is a bug that we could perhaps fix if you would be so kind as
> to report it at https://redmine.gromacs.org.
>
> But the core problem remains that something about how you sampled didn't
> meet the expectations of gmx wham.
>
> Mark
>
> On Wed, Mar 14, 2018, 15:45 Ben Tam <btam125 at hotmail.co.uk> wrote:
>
> > Dear all,
> >
> > I have a rather strange problem. Currently I am trying to get a PMF of a
> > water molecule through a hydrophobic materials. At the end of using "gmx
> > wham", I get a rather good histogram and it cover the whole range of the
> > system. However at the making profile.xvg. I get the answer "nan" inside
> > the file. Therefore I really cannot think of why is it giving me that?
> >
> > Currently I set it as :
> > ;Pull code
> > pull = yes
> > ;pull-cylinder-r = 0.5
> > pull_ngroups = 2
> > pull_ncoords = 1
> > pull_group1_name = SOL
> > pull_group2_name = MOL
> > pull_coord1_type = umbrella ; harmonic biasing force
> > pull_coord1_geometry = direction-periodic ; simple distance increase,
> > direction-periodic
> > pull_coord1_vec = 1 1 1
> > pull_coord1_groups = 1 2
> > pull_coord1_dim = Y Y Y
> > pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
> > pull_coord1_k = 10000 ; kJ mol^-1 nm^-2
> > pull_coord1_start = yes ; define initial COM distance > 0
> >
> > Also this appears when I used the command "gmx wham":
> >
> > Switched to exact iteration in iteration 1
> >            1) Maximum change -1.000000e+20
> > Converged in 2 iterations. Final maximum change -1e+20
> >
> > Therefore I really don't understand what I have to do in order to get a
> > profile.xvg. I understand the k value is high, but without that high
> value,
> > the water won't settle within the assign window.
> >
> > Am I doing something wrong? because I got a good histogram but no result
> > in the profile.xvg? Thank you very much for your help.
> >
> > Best regards,
> >
> > Ben
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 167, Issue 74
> ******************************************************
>

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