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

Mon Mar 9 16:33:51 CET 2015

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?

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!
> >
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> >
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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
> ******************************************************
>