From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 06 2012 - 09:23:01 CST
And just in case JC's correct answer isn't enough for you ... this question
was previously answered on Feb 9 (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/15960.html),
providing the below tcl scripted solution which should always work no
matter what source file was used to load the frame. Please remember to
search the listserv (http://www.ks.uiuc.edu/Research/namd/mailing_list/)
for possible answers.
Best,
Chris
In the console enter the below function or
else save it in a text file and from the console type: source
directoryToYourTextFile/nameOfYourTextFile.
proc get_cell {{molid top}} {
set all [atomselect $molid all]
set minmax [measure minmax $all]
set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]
puts "cellBasisVector1 [lindex $vec 0] 0 0"
puts "cellBasisVector2 0 [lindex $vec 1] 0"
puts "cellBasisVector3 0 0 [lindex $vec 2]"
set center [measure center $all]
puts "cellOrigin $center"
$all delete
}
Now make sure your molecule is the top molecule in VMD (ie has the T
in it's line in the "VMD Main" window). Then in the console type:
get_cell. The basis vectors for your system should be output.
Best,
Chris
On Tue, Mar 6, 2012 at 9:00 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> And to further clarify, VMD reads them from the dcd and can be accessed
> using
>
> molinfo top get a (b and c)
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Axel Kohlmeyer
> Sent: Tuesday, March 06, 2012 8:53 AM
> To: Aron Broom
> Cc: mjyang; namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: how to calculate the box size
>
> On Tue, Mar 6, 2012 at 9:44 AM, Aron Broom <broomsday_at_gmail.com> wrote:
> > What if for the water molecules in your system you calculate from the
> > center of mass of the waters rather than just the atomic coordinates?
> > I don't know what the real answer is, but that would shrink your box ever
> so slightly.
>
> that is nonsense. you cannot reconstruct the box size from the positions
> of
> the atoms. full stop. but the box dimensions are usually stored in the dcd
> trajectory file. those are the only ones you can use or those in a proper
> .xsc file.
>
> axel.
>
> >
> >
> > On Tue, Mar 6, 2012 at 2:48 AM, mjyang <mjyang_at_hku.hk> wrote:
> >>
> >> Dear NAMD users,
> >>
> >> I performed a simulation by NAMD for a protein system solvated by
> >> a cubic water box. Now I extracted the snapshots from NAMD trajectory
> >> for postpone analysis, in which the protein should be centered in the
> >> box. The box size was calculated by (max_x-min_x, max_y-min_y,
> >> max_z-min_z), where max_x,y,z and min_x, y, z are the maximum and
> >> minimum coordinate values of the extracted frame. However, the box
> >> size calculated in this way is a little larger than the real one,
> >> resulting in gaps in the recentered box. It seems that the box size
> >> written out by NAMD in the *.xsc file is better than what I
> >> calculated. But the NAMD output size (in *.xsc file) only corresponds
> >> to the last frame of a segment of trajectory file and I need the size
> >> for each frame in the traj. Could someone please tell me how NAMD
> calculate the box along MD simulations?
> >>
> >>
> >> Many thanks.
> >>
> >>
> >> Mingjun
> >>
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:44 CST