[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41

Mon Mar 9 18:29:02 CET 2015

On Mon, Mar 9, 2015 at 4:33 PM, Xingcheng Lin <linxingcheng50311 at gmail.com>
wrote:

> Hi Mark,
>
> -cl only gives me the central structure of that cluster. What I need is an
> expanded .xtc file with every structure in that cluster. Is there any way
> to realize that?
>

Yes, as documented in gmx cluster -h in the part that talks about -cl plus
some other optional flags. :-)

Mark

> Thank you,
> Xingcheng
>
>
> On Mon, Mar 9, 2015 at 6:00 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> >
> >
> > Today's Topics:
> >
> >    1. Re: Separate .xtc file according to the result from       g_cluster
> >       (Mark Abraham)
> >    2. definition of "eigenvector" in gromacs (Brett)
> >    3. adding metal ion (Meenakshi Rajput)
> >    4. Re: definition of "eigenvector" in gromacs (Tsjerk Wassenaar)
> >    5. Re: definition of "eigenvector" in gromacs (ms)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 9 Mar 2015 02:04:47 +0100
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Separate .xtc file according to the result
> >         from    g_cluster
> > Message-ID:
> >         <
> > CAMNuMATwzvNRpfbJYEb3jdX6WjbT_sZFt2JMGq7o-4KzeKerjQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > gmx cluster -h is a good friend ;-) see the -cl option.
> >
> > Mark
> >
> > On Mon, Mar 9, 2015 at 1:49 AM, Xingcheng Lin <
> linxingcheng50311 at gmail.com
> > >
> > wrote:
> >
> > > Hi,
> > >
> > > Is there any short way to seperate the .xtc file according to the
> results
> > > from g_cluster? For example, I want to chop the .xtc file into several
> > > small trajectories, each includes all the snapshots from the clusters
> > given
> > > by g_cluster?
> > >
> > > Thank you,
> > > --
> > > 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.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 9 Mar 2015 09:33:16 +0800 (CST)
> > From: Brett <brettliu123 at 163.com>
> > To: gmx-users <gmx-users at gromacs.org>
> > Subject: [gmx-users] definition of "eigenvector" in gromacs
> > Message-ID: <77570a06.253b.14bfc2a2adc.Coremail.brettliu123 at 163.com>
> > Content-Type: text/plain; charset=GBK
> >
> > Dear All,
> >
> > Recently I have read a gromacs related article which contain a sentence
> > "Trajectories pojected on the first two eigenvectors". Will you please
> tell
> > me the meaning of "eigenvector" and "Trajectories pojected on the first
> two
> > eigenvectors"? Will you please also explain it to me using common-used
> > words simple as desk, meal, earth, etc?
> >
> > Brett
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 9 Mar 2015 13:41:01 +0530
> > From: Meenakshi Rajput <ashi.rajput39 at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] adding metal ion
> > Message-ID:
> >         <
> > CAH5GTBKE-72AYBoCtZH91Jdq5z0_EW8NHmGBgMRvxZy6Aug2wQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > hello users
> > I need to add selenium ion in the protein complex. Can anyone tell me how
> > to add a metal ion in gromacs? I posted the question before but I didn't
> > get any reply so I am posting again. Please tell me if anybody knows.
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Mon, 9 Mar 2015 10:19:21 +0100
> > From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] definition of "eigenvector" in gromacs
> > Message-ID:
> >         <
> > CABzE1SjzO4e+6OmB8_T_H3htVhJpr3M7WNpyVJcZNe+GmFkxmg at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Brett,
> >
> > Let's say you're sitting at your _desk_ writing that paper with a
> deadline
> > yesterday and you put a quick _meal_ next to you, wondering why on
> _earth_
> > you keep up with this. Your hands are moving between the meal and the
> > keyboard. You notice that the average position of your hands is somewhere
> > between the two and mark the mean position on your desk. Then you draw a
> > line through it that corresponds to the major extent of the motion of
> your
> > hands, and write 'eigenvector 1' along it. You add a line through the
> > average position, perfectly perpendicular to the first, and write
> > 'eigenvector 2' along it. Now you can project every position of your
> hands
> > onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an
> > 'eigenvector 2' coordinate (or score). You notice that it's only part of
> > the total motion, as you neglect the height, which will be a third line,
> > perpendicular to the desk.
> >
> > You can look at it a bit differently and say that your desk is the
> subspace
> > of your real space, spanned by the two perpendicular vectors, which
> > together describe most of your hand's motion.
> >
> > I hope this makes some sense :)
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> >
> >
> >
> > On Mon, Mar 9, 2015 at 2:33 AM, Brett <brettliu123 at 163.com> wrote:
> >
> > > Dear All,
> > >
> > > Recently I have read a gromacs related article which contain a sentence
> > > "Trajectories pojected on the first two eigenvectors". Will you please
> > tell
> > > me the meaning of "eigenvector" and "Trajectories pojected on the first
> > two
> > > eigenvectors"? Will you please also explain it to me using common-used
> > > words simple as desk, meal, earth, etc?
> > >
> > > Brett
> > >
> > >
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Mon, 09 Mar 2015 11:04:41 +0100
> > From: ms <devicerandom at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] definition of "eigenvector" in gromacs
> > Message-ID: <54FD7039.8040602 at gmail.com>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > I am gluing this email exchange to my office wall. This is just awesome.
> > Thanks to you all.
> >
> > On 3/9/15 10:19 AM, Tsjerk Wassenaar wrote:
> > > Hi Brett,
> > >
> > > Let's say you're sitting at your _desk_ writing that paper with a
> > deadline
> > > yesterday and you put a quick _meal_ next to you, wondering why on
> > _earth_
> > > you keep up with this. Your hands are moving between the meal and the
> > > keyboard. You notice that the average position of your hands is
> somewhere
> > > between the two and mark the mean position on your desk. Then you draw
> a
> > > line through it that corresponds to the major extent of the motion of
> > your
> > > hands, and write 'eigenvector 1' along it. You add a line through the
> > > average position, perfectly perpendicular to the first, and write
> > > 'eigenvector 2' along it. Now you can project every position of your
> > hands
> > > onto your desk, giving it an 'eigenvector 1' coordinate (or score) and
> an
> > > 'eigenvector 2' coordinate (or score). You notice that it's only part
> of
> > > the total motion, as you neglect the height, which will be a third
> line,
> > > perpendicular to the desk.
> > >
> > > You can look at it a bit differently and say that your desk is the
> > subspace
> > > of your real space, spanned by the two perpendicular vectors, which
> > > together describe most of your hand's motion.
> > >
> > > I hope this makes some sense :)
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > >
> > >
> > >
> > >
> > > On Mon, Mar 9, 2015 at 2:33 AM, Brett <brettliu123 at 163.com> wrote:
> > >
> > >> Dear All,
> > >>
> > >> Recently I have read a gromacs related article which contain a
> sentence
> > >> "Trajectories pojected on the first two eigenvectors". Will you please
> > tell
> > >> me the meaning of "eigenvector" and "Trajectories pojected on the
> first
> > two
> > >> eigenvectors"? Will you please also explain it to me using common-used
> > >> words simple as desk, meal, earth, etc?
> > >>
> > >> Brett
> > >>
> > >>
> > >> --
> > >> 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 131, Issue 41
> > ******************************************************
> >
> --
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