From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Sep 03 2013 - 04:55:03 CDT
I hope you are joking. You will not get the correct structure if you don't
use the box dimensions you used during the simulation, what you are doing is
simply wrong. It seems you have no idea of how a periodic box and a
molecular simulation actually works. If your box was too small during the
simulation, so that your solute couldn't fit into the box without
overlapping with the box boundaries, you will simply not be able to wrap it
in a way, that you won't see the overlong bonds anymore. Is it so hard to
understand? Please take some time and think about, what is expected to
happen with a too big molecule in a periodic box.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: jinxj [mailto:jinxj10_at_lzu.edu.cn]
> Gesendet: Dienstag, 3. September 2013 11:45
> An: Norman Geist
> Betreff: Re: AW: AW: namd-l: pbc error
>
> Dear professor:
>
> The box was set larger and the wrap was repeated. The command
> lines is :
>
> pbc set {100 100 150} -all
> pbc wrap -all -compound res -center com -centersel all
>
> When the last "all" was removed, the present frame was ok and the wrap
> succeeded.
> Unfortunately, when the last "all" was preserved, the wrap was run on
> all frames and finally failed.
> Was there any solution for this problem?
>
> Xiaojie
>
> > -----原始邮件-----
> > 发件人: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> > 发送时间: 2013-09-02 17:54:23 (星期一)
> > 收件人: 'jinxj' <jinxj10_at_lzu.edu.cn>
> > 抄送:
> > 主题: AW: AW: namd-l: pbc error
> >
> > It's enough to wrap one time only. If your selection was correct and
> there
> > are still parts of your solute that stick out of the box, your box
> might be
> > too small for your structure to entirely fit into.
> >
> > Norman Geist.
> >
> > > -----Ursprüngliche Nachricht-----
> > > Von: jinxj [mailto:jinxj10_at_lzu.edu.cn]
> > > Gesendet: Montag, 2. September 2013 11:07
> > > An: Norman Geist
> > > Betreff: Re: AW: namd-l: pbc error
> > >
> > > Dear professor:
> > > Thanks for your enthusiastic help. When I repeated the pbc
> command
> > > line below for 12 times, the structures were viewed easonable and
> > > centered. However, there are some small segments that is separated
> from
> > > the main protein.
> > >
> > > The command used is :"pbc wrap -all -compound res -center com -
> > > centersel all"
> > >
> > >
> > >
> > >
> > > > -----原始邮件-----
> > > > 发件人: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> > > > 发送时间: 2013-09-02 14:44:18 (星期一)
> > > > 收件人: 'jinxj' <jinxj10_at_lzu.edu.cn>
> > > > 抄送: "Namd Mailing List" <namd-l_at_ks.uiuc.edu>
> > > > 主题: AW: namd-l: pbc error
> > > >
> > > > If you have more than only the pentamer in your cell, "-centersel
> > > all" will
> > > > NOT do anything. Try to select you pentamer only for the
> centering
> > > maybe
> > > > "-centersel protein" or similar. The effects you see are just
> normal
> > > and
> > > > they must occur if parts of you molecule cross the bounds of a
> > > periodic box.
> > > > If the problem persists, your box might simply be too small. You
> > > should do
> > > > some deeper thinking how pbc actually works to understand and
> predict
> > > the
> > > > behavior you see.
> > > >
> > > > Norman Geist.
> > > >
> > > > > -----Ursprüngliche Nachricht-----
> > > > > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> Im
> > > > > Auftrag von jinxj
> > > > > Gesendet: Montag, 2. September 2013 04:39
> > > > > An: namd
> > > > > Betreff: namd-l: pbc error
> > > > >
> > > > >
> > > > > Dear professor:
> > > > >
> > > > > We simulated a pentamer protein with NAMD. I am confused
> about
> > > that
> > > > > some part of the pemtamer fluctuated in and out of the box when
> I
> > > > > viewed the trajectory in VMD. Then I dealed with pbctools in
> vmd
> > > and
> > > > > failed. The command used are at below.
> > > > >
> > > > > package require pbctools
> > > > > pbc wrap -all -compound res -center com -centersel all
> > > > >
> > > > > After this operation, all parts of the protein was centered.
> But
> > > > > there are errors in some of the structures. When I viewed the
> > > treated
> > > > > trajectory in VMD, the unrecognizable structure coordinates
> were
> > > > > generated.
> > > > > What can I do about this problem?
> > > > >
> > > > > Xiaojie
> > > >
> >
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