AMBER Archive (2003)

Subject: RE: Periodic Box

From: Xiang, Tian-Xiang (txian2_at_email.uky.edu)
Date: Sat Feb 08 2003 - 10:52:49 CST

the first number is the angle of the cell, 90 degree. Apparently, you used a cubic cell so all three angles are 90 degree.
 
the periodic boundary conditions used minimum imgae convention. The coordiantes look like far apart but the two fragments are still in the central box. To get the right coordinates in the center box, use "ptraj" program and the "image center" command in the program.
 
Tian-xiang Xiang

        -----Original Message-----
        From: John Finke [mailto:jfinke_at_chem.ucsd.edu]
        Sent: Fri 2/7/2003 7:25 PM
        To: amber_at_heimdal.compchem.ucsf.edu
        Cc:
        Subject: Periodic Box
        
        

        Hello,
        
        I have an AMBER problem which I am having some difficulty,
        
        I am using sander_classic to run MD on 2 separate peptide fragments and
        intend to use a periodic box to keep them close to one another and avoid
        them flying away from one another.
        
        I have followed the tutorial examples as much as possilble to create a
        periodic box (with no waters). The dimensions of this box are listed at
        the last line of the topology parmtop file.
        
          0.90000000E+02 0.34297554E+02 0.33792557E+02 0.34400002E+02
        
        I don't know what the first number is but the next three are the x, y, z
        dimensions of the box.
        
        In any event, it appears that sander is ignoring the box as the 2 peptides
        simply end up flying away from each other (at distances farther than the
        box). I have made sure my imput &cntrl parameter specifies ntb = 1 (which
        should be sufficient, right?)
        
        If anyone has had experience using periodic boxes with sander_classic, I
        would appreciate any advice they could give me.
        
        Thanks.
        
        Sincerely,
        
        
        John Finke