**From:** Ajasja Ljubetič (*ajasja.ljubetic_at_gmail.com*)

**Date:** Tue Mar 06 2012 - 09:32:43 CST

**Next message:**Chris Harrison: "Re: how to calculate the box size"**Previous message:**Chris Harrison: "Re: how to calculate the box size"**In reply to:**Chris Harrison: "Re: how to calculate the box size"**Next in thread:**Chris Harrison: "Re: how to calculate the box size"**Reply:**Chris Harrison: "Re: how to calculate the box size"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

But this script is using measure minmax, so in principle this is the same

as trying to reconstruct the periodic box from atomic coordinates (correct

me if I'm wrong).

I think a better version is:

proc get_cell {{molid top}} {

puts "cellBasisVector1 [molinfo $molid get a] 0 0"

puts "cellBasisVector2 0 [molinfo $molid get b] 0"

puts "cellBasisVector3 0 0 [molinfo $molid get c]"

set all [atomselect $molid all]

puts "cellOrigin [measure center $all] "

$all delete

}

On Tue, Mar 6, 2012 at 16:23, Chris Harrison <charris5_at_gmail.com> wrote:

*> 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
*

*>
*

*>
*

*>
*

*>
*

**Next message:**Chris Harrison: "Re: how to calculate the box size"**Previous message:**Chris Harrison: "Re: how to calculate the box size"**In reply to:**Chris Harrison: "Re: how to calculate the box size"**Next in thread:**Chris Harrison: "Re: how to calculate the box size"**Reply:**Chris Harrison: "Re: how to calculate the box size"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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