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

2016-10-09 Thread 胡杰 
Dear Tsjerk，

I visually checked the trajectory(md_backbone.xtc) in VMD and there is no 
break. Actually I spelled wrong that md1_backbone.xtc and md_backbone.xtc is 
the same.

Best regards,

Jie





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

2016-10-08 Thread Tsjerk Wassenaar 
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  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-requ...@maillist.sys.kth.se
> > 发送时间: 2016年10月7日 星期五
> > 收件人: gromacs.org_gmx-users@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@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-requ...@maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> >  gromacs.org_gmx-users-ow...@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 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Umbrella sampling tutorial
> > Message-ID: 
> > 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: ?? 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] principal  component analysis chain break
> > Message-ID:
> >  <612918.790a.1579e71fe59.coremail.huji...@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 
> > To: Discussion list for GROMACS users 
> > Subject: Re: [gmx-users] principal component analysis chain break
> > Message-ID:
> >

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

2016-10-08 Thread 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-requ...@maillist.sys.kth.se
> 发送时间: 2016年10月7日 星期五
> 收件人: gromacs.org_gmx-users@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@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-requ...@maillist.sys.kth.se
> 
> You can reach the person managing the list at
>  gromacs.org_gmx-users-ow...@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 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Umbrella sampling tutorial
> Message-ID: 
> 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: ?? 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] principal  component analysis chain break
> Message-ID:
>  <612918.790a.1579e71fe59.coremail.huji...@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 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] principal component analysis chain break
> Message-ID:
>