RE: Cell Basis Vectors

From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Mon Jul 05 2004 - 09:46:24 CDT

Yes, you can use "measure minmax" in VMD to get the box dimensions. You should preferably use cell basis vectors a little larger than the the numbers you get from the "measure minmax" command, to prevent 'clashes' between water molecules between your simulation system and the images (although minimization might solve these). See also the example of the config-file with periodic boundary conditions from the tutorial files (ubq_wb_eq.conf and p.20 in the tutorial).
 
good luck,
Marc

        -----Original Message-----
        From: owner-namd-l_at_ks.uiuc.edu on behalf of Raymond C. Fort Jr.
        Sent: Mon 5-7-2004 14:57
        To: namd-l_at_ks.uiuc.edu
        Cc:
        Subject: namd-l: Cell Basis Vectors
        
        

        How does one determine the cell basis vectors when setting up a simulation
        in a periodic box? I have used the "measure minmax" command to obtain the
        dimensions of the box. Am I correct to assume that these are the numbers I
        need?
        
        Thanks for any help!
        
        Ray
        
        
        Professor Ray Fort Jr. rcfort_at_maine.edu
        Department of Chemistry chemistry.umeche.maine.edu/fort.html
        University of Maine Voice: (207)-581-1180
        Orono, ME 04469 FAX: (207)-581-1191
        
        Computer modeling of organic and biomolecules; chemistry of lignin
        and cellulose
        
        
        

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