Re: how to calculate the box size

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Mar 06 2012 - 09:32:43 CST

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
>
>
>
>

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