Re: colvar restrain of water in lipid system

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 29 2011 - 09:36:39 CDT

Hello Emilia, is there any error or warning message before "Error: no
collective variables defined."? There should be.

Please also beware that the way you set up the system you only apply a
restraint on the center of mass of the water layer, but individual waters
can still diffuse!

For how tedious as this may sound, you need to create two such variables *for
each water molecule in the system*.

On Mon, Aug 29, 2011 at 10:13 AM, Ling Wu <emilia.l.wu_at_gmail.com> wrote:

> 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
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:21 CST