colvar restrain of water in lipid system

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Mon Aug 29 2011 - 09:13:58 CDT

Hi All,

Sorry for posting this message again, but could anyone give me any suggestion on this, thanks a lot!

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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