From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 24 2007 - 13:52:43 CST

On Wed, 24 Jan 2007, Akshay Patny wrote:

AP> Hi Axel
AP>
AP> I did following:
AP> --------------------------------------------------------------------------------------------------------------
AP> Main console display active (Tcl8.4.1 / Tk8.4.1)
AP> (Desktop) 26 % set sel [atomselect top all]
AP> atomselect0
AP> >Main< (Desktop) 27 % measure minmax $sel
AP> {-12.9750003815 -5.4439997673 -0.989000022411} {119.277000427
AP> 106.664001465 74.4410018921}
AP> --------------------------------------------------------------------------------------------------------------
AP>
AP> Thus I got following XYZ dimensions for my system:
AP>
AP> x = 132.2520008085
AP> y = 112.1080012323
AP> z = 75.430001914511
AP>
AP> Now, as you suggested the atom diameters are not calculated, so do you
AP> recommend adding 5 A in each dimension (or may be less like 2 or 3 A).

you'll have to do a variable cell MD anyways to get the system to
an equilibrium density anyways, so a little more won't hurt.

a good way to check your results empirically is to use

molinfo top set {a b c} {136.0 116.0 80.0}

to make VMD aware of your unitcell dimensions
and then turn on peridic display (best with
VDW representation, if you graphics card can
handle it and you are patient enough) and check
for overlaps at the boundaries.

cheers,
   axel.

AP>
AP> Thanks for your suggestions.
AP>
AP> Best Regards, -Akshay
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>
AP> -----Original Message-----
AP> From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
AP> Sent: Wednesday, January 24, 2007 12:14 PM
AP> To: Akshay Patny
AP> Cc: vmd-l_at_ks.uiuc.edu
AP> Subject: Re: vmd-l: measure XYZ dimensions of a system
AP>
AP> On Wed, 24 Jan 2007, Akshay Patny wrote:
AP>
AP> AP> Hi All
AP> AP>
AP> AP> I want to place my system in a periodic box using TLEAP in AMBER using
AP> AP> "set box" command to later run a PBC NPT MD simulation.
AP> AP>
AP> AP> For that I need to calculate the XYZ dimensions of my system, can
AP> AP> somebody tell me how can we calculate X, Y and Z dimensions of current
AP> AP> system loaded in VMD. I have the TOP and CRD files.
AP>
AP> try:
AP>
AP> measure minmax
AP>
AP> you may want to add some safety to the results as this does not
AP> take into account the 'diameter' of atoms.
AP>
AP> cheers,
AP> axel.
AP>
AP> AP>
AP> AP> Thanks, I look forward to hear from you.
AP> AP>
AP> AP> Best Regards
AP> AP> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
AP> AP> Akshay Patny
AP> AP> PhD Candidate (5th Yr.), Computational Chemistry
AP> AP> Department of Medicinal Chemistry, School of Pharmacy
AP> AP> The University of Mississippi
AP> AP> 805 College Hill Rd, # 9, Oxford, MS 38655
AP> AP> E-mail: akshay17_at_olemiss.edu
AP> AP> Phone (O): (662)-915-1286,(M): (662)-801-5496
AP> AP> = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
AP> AP>
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
=======================================================================
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