[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67

[Jian Zou]

set sel [atomselect $molid "selection"]

for {set iframe 0} {$iframe < $nframe} {incr iframe} {
    $sel frame $iframe
    $sel update
    $sel get {the property you want}
}

you may go to vmd mailing list for more details.

>  Message: 1
>  Date: Tue, 22 Apr 2008 10:42:56 +0800
>  From: Dechang Li <li.dc06 at gmail.com>
>  Subject: [gmx-users] Re: the number of water molecules (Jian Zou)
>  To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>  Message-ID: <480d50ba.25bc720a.5a70.fffffdf0 at mx.google.com>
>  Content-Type: text/plain;       charset="gb2312"
>
>
>  >
>  >Message: 2
>  >Date: Mon, 21 Apr 2008 10:43:27 -0400
>  >From: "Jian Zou" <jianzou at gmail.com>
>  >Subject: [gmx-users] Re: the number of water molecules
>  >To: gmx-users at gromacs.org
>  >Message-ID:
>  >       <cacdffa50804210743o24ab6a03m7c9660bd5b0af802 at mail.gmail.com>
>  >Content-Type: text/plain; charset=ISO-8859-1
>  >
>  >How about using vmd selection "within" to do this
>
>   I have tried this. However, vmd can tell me the number in this
>  frame, but there are about 5000 frames! I am tring to write a script
>  to let vmd explore the results to a file VS. frames. If I make
>  any progress, let you know. ^_^
>
>
>  >
>  >>  Message: 3
>  >>  Date: Sun, 20 Apr 2008 21:01:57 +0800
>  >>  From: Dechang Li <li.dc06 at gmail.com>
>  >>  Subject: [gmx-users] the number of water molecules
>  >>  To: "gmx-users" <gmx-users at gromacs.org>
>  >>  Message-ID: <480b3ecc.25d7720a.4f8d.ffffb16a at mx.google.com>
>  >>  Content-Type: text/plain;       charset="gb2312"
>  >>
>  >>  Dear all,
>  >>
>  >>     How can I calculate the number of water molecules around the
>  >>  protein with a distance about 5 angstrom? Is that possible in
>  >>  Gromacs?
>  >>
>  >>
>  >>
>  >>  Best regards,
>  >>
>  >>  2008-4-20
>  >>
>  >>
>  >>  =========================================
>  >>  Dechang Li, PhD Candidate
>  >>  Department of Engineering Mechanics
>  >>  Tsinghua University
>  >>  Beijing 100084
>  >>  PR China
>  >>
>  >>  Tel:   +86-10-62773779(O)
>  >>  Email: lidc02 at mails.tsinghua.edu.cn
>  >>  =========================================
>  >>
>  >
>  >
>  >------------------------------