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

Sat Oct 8 15:58:05 CEST 2016

Hi Jie,

Knowing a few words is not yet knowing the language :)
It's a bit odd that the extreme projections, or any projection for that
matter, has breaks where the original has bonds. Projecting on any subset
of principal components is a reduction of dimensionality and distances
between particles can thus only become smaller. Have you visually checked
the trajectory? What's the difference between md_backbone.xtc and
md1_backbone.xtc?

Cheers,

Tsjerk

On Sat, Oct 8, 2016 at 3:33 PM, 胡杰 <hujie14 at mails.ucas.ac.cn> wrote:

> 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
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> > Today's Topics:
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> >    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
> > >
> > >
> > >
> > >
> > >
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-- 
Tsjerk A. Wassenaar, Ph.D.