VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 24 2007 - 12:13:42 CST

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.