colvar restrain of water in lipid system

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Fri Aug 26 2011 - 14:44:21 CDT

Hi All,

I have a question about using colvar to do MD simulation. I am working on a lipid bilayer system, what I am trying to do is restrain the water molecule from going into the hydrophobic core of my system.
so I used 2 colvar restrain to control the water on the top and the water on the bottom separately. For water with Z coordinate bigger than 0, I tried to keep it in the range of 35 > Z >11, and it works fine. But
for the water with Z coordinate smaller than 0, I want to keep them in the range of -11 > Z > -35, but it did not work, I copied my colvar file below, and the error message is here. can anyone tell me what's going on here?
Thanks a lot!
-------------------------------------------------------------------------------------------
colvars: Error: no collective variables defined.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
------------------------------------------------------------------------------------------

 
colvar {
    name waterup
    width 0.1
    lowerboundary 11.0
    upperboundary 35.0
    lowerWall 11.0
    upperWall 35.0
    lowerWallConstant 2.5
    upperWallConstant 2.5
    distanceZ {
        main {
           atomsFile watup_main.ref # use Tcl script to generate this file with selection of all the waters #
             atomsCol B
             atomsColValue 1.0
         }
        ref {
           dummyAtom ( 0.000, 0.000, 0.000 )
         }
          axis (0.0, 0.0, 1.0)
    }
 }

colvar {
    name waterdown
    width 0.1
    lowerboundary -35.0
    upperboundary -11.0
    lowerWall -35.0
    upperWall -11.0
    lowerWallConstant 2.5
    upperWallConstant 2.5
    distanceZ {
        main {
           atomsFile watdown_main.ref # use Tcl script to generate this file with selection of all the waters #
             atomsCol B
             atomsColValue 1.0
         }
        ref {
           dummyAtom ( 0.000, 0.000, 0.000 )
         }
          axis (0.0, 0.0, 1.0)
    }

Emilia

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