From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Aug 31 2012 - 19:55:42 CDT
Patrick Chiu <patrick817us_at_yahoo.com> writes:
> Date: Fri, 31 Aug 2012 16:45:19 -0700 (PDT)
> From: Patrick Chiu <patrick817us_at_yahoo.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: The size of a periodic cell in NAMD operation
> X-Mailer: YahooMailClassic/15.0.8 YahooMailWebService/0.8.121.416
>
> Dear Sir/Madam:
> How do I decide the size of a periodic cell in NAMD operation. Is it just big enough to hold the model containing protein and waters?
> Yours sincerely
> NAMD user
> See Hong Chiu
>
Typically, yes.
If you put the below proc in a file (get_cell.tcl) and load it into the
TkConsole (see Extensions > TkConsole) in VMD with "source get_cell.tcl", then
load your system and finally type in the TkConsole get_cell, it will output the
necessary vectors and center.
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
}
Best,
Chris
-- 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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