[gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

[胡杰]

Hi Tsjerk,
Thanks for your reply. It's amazing you know my language!
I'm sure PBC is processed, and the input trajectory is whole. But, chain do break in extreme projection.
By the way could you please give me some suggestions about meaningful PCA output. 
Sincerely yours
Jie


> -----原始邮件-----
> 发件人: gromacs.org_gmx-users-request at maillist.sys.kth.se
> 发送时间: 2016年10月7日 星期五
> 收件人: gromacs.org_gmx-users at maillist.sys.kth.se
> 抄送: 
> 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 35
> 
> 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. Umbrella sampling tutorial (gozde ergin)
>    2. principal  component analysis chain break (??)
>    3. Re: principal component analysis chain break (Tsjerk Wassenaar)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 7 Oct 2016 10:41:36 +0200
> From: gozde ergin <gozdeeergin at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Umbrella sampling tutorial
> Message-ID: <DB4C74AD-BC61-436B-877E-5D940F83FFE8 at gmail.com>
> Content-Type: text/plain; charset=utf-8
> 
> Dear all,
> 
> I would like to ask a question about Justin?s tutorial.
> By using the POSRES_B, a restraint is applied on chain B in order to immobile it. Is the effect of this restraint removed during the WHAM? 
> 
> I want to do a similar thing by applying restraint force on the organic molecule on the bulk water in order to inhibit their movement inside the bulk. Should I consider the removing of the restraint in PMF?
> 
> Thanks in advance.
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 7 Oct 2016 17:20:53 +0800 (GMT+08:00)
> From: ?? <hujie14 at mails.ucas.ac.cn>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] principal  component analysis chain break
> Message-ID:
>  <612918.790a.1579e71fe59.Coremail.hujie14 at mails.ucas.ac.cn>
> Content-Type: text/plain; charset=GBK
> 
> Dear Gromacs community,
> 
> It's a question about principal  component analysis(PCA).
> Starting with a tRNA trajectory xtc file and a reference pdb file I use the following command, :
> 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb -first 1 -last 1 -nframes 30
> 
> extreme1.pdb is what I want, but the chain of the structure break at some place showing from PLMOL or VMD. What's the matter. Could you please tell me how to get the compelet structure of extreme1.pdb.
> 
> best regards
> Jie
> 
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 7 Oct 2016 11:34:46 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] principal component analysis chain break
> Message-ID:
>  <CABzE1SgrTeu9=Ngr6J3zXJ6+YG89wC4J_E2t-cDrXE4ieX_kbg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Ni hao Jie,
> 
> The extreme projections are typically pretty meaningless. But if you want
> them or the more meaningful PCA output, do make sure you remove jumps over
> PBC from your input trajectory and have the molecules whole/clustered.
> 
> Cheers,
> 
> Tsjerk
> 
> On Oct 7, 2016 11:21 AM, "??" <hujie14 at mails.ucas.ac.cn> wrote:
> 
> > Dear Gromacs community,
> >
> > It's a question about principal  component analysis(PCA).
> > Starting with a tRNA trajectory xtc file and a reference pdb file I use
> > the following command, :
> > 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> > 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb
> > -first 1 -last 1 -nframes 30
> >
> > extreme1.pdb is what I want, but the chain of the structure break at some
> > place showing from PLMOL or VMD. What's the matter. Could you please tell
> > me how to get the compelet structure of extreme1.pdb.
> >
> > best regards
> > Jie
> >
> >
> >
> >
> >
> > --
> > 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 150, Issue 35
> ******************************************************