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From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Wed Jan 24 2007 - 12:47:47 CST
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Hi Axel
I did following:
--------------------------------------------------------------------------------------------------------------
Main console display active (Tcl8.4.1 / Tk8.4.1)
(Desktop) 26 % set sel [atomselect top all]
atomselect0
>Main< (Desktop) 27 % measure minmax $sel
{-12.9750003815 -5.4439997673 -0.989000022411} {119.277000427
106.664001465 74.4410018921}
--------------------------------------------------------------------------------------------------------------
Thus I got following XYZ dimensions for my system:
x = 132.2520008085
y = 112.1080012323
z = 75.430001914511
Now, as you suggested the atom diameters are not calculated, so do you
recommend adding 5 A in each dimension (or may be less like 2 or 3 A).
Thanks for your suggestions.
Best Regards, -Akshay
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
Sent: Wednesday, January 24, 2007 12:14 PM
To: Akshay Patny
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: measure XYZ dimensions of a system
On Wed, 24 Jan 2007, Akshay Patny wrote:
AP> Hi All
AP>
AP> I want to place my system in a periodic box using TLEAP in AMBER using
AP> "set box" command to later run a PBC NPT MD simulation.
AP>
AP> For that I need to calculate the XYZ dimensions of my system, can
AP> somebody tell me how can we calculate X, Y and Z dimensions of current
AP> system loaded in VMD. I have the TOP and CRD files.
try:
measure minmax
you may want to add some safety to the results as this does not
take into account the 'diameter' of atoms.
cheers,
axel.
AP>
AP> Thanks, I look forward to hear from you.
AP>
AP> Best Regards
AP> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
AP> Akshay Patny
AP> PhD Candidate (5th Yr.), Computational Chemistry
AP> Department of Medicinal Chemistry, School of Pharmacy
AP> The University of Mississippi
AP> 805 College Hill Rd, # 9, Oxford, MS 38655
AP> E-mail: akshay17_at_olemiss.edu
AP> Phone (O): (662)-915-1286,(M): (662)-801-5496
AP> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
AP>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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