Re: restraint with colvars mocule

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Sep 12 2011 - 04:48:33 CDT

Hi Emilia,

>From your input, one would expect the center of the whole membrane to
shift to z=19 A eventually. To achieve what you want, you need two
variables, one for each leaflet, and restrain one to +19 and the other
to -19.

Cheers,
Jerome

On 11 September 2011 23:25, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> Hi All,
>
> I have a question regarding the colvars function of NAMD.
>
> I am trying to run a simulation of a pure POPC membrane system. I want to enforce a positional restrain on the head group and the tail group of POPC to constrain them at a certain area along Z-axis for the initial equilibration. After I apply this restrain on the system, I checked if the center of mass of the head group or tail group is in the area I want  (head: +19 and -19; tail: between +5 and -5), but what I found is the membrane atoms are all shift up after 25ps MD, even though the center of the entire system (membrane+water+ion) is 0, 0, 0, but the center of the membrane shift to like 0, 0, 2. when I looked at the structure in VMD, it is obvious that there are thinner layer of water on the top of the membrane, and a much thicker layer of water on the bottom.  I also found the bigger force constant I used, the more the center will shift up. if I remove the colvar part from my input file, then there is no prolem.
>
> here is  my ColvarsConfig,
>
> ##Lipid Head###
>
> Colvarstrajfrequency 100
> Colvarsrestartfrequency 100
>
> colvar {
>   name head_POPC
>   distanceZ {
>      ref {
>         dummyAtom ( 0.000, 0.000, 0.000 )
>      }
>       main {
>             atomsFile head_POPC_main.ref   # head atoms #
>             atomsCol    B
>             atomsColValue      1.0
>         }
>   }
> }
> harmonic {
>  colvars head_POPC
>  centers 19 # or wherever the head group should be (15, 18, 17...) #
>  forceConstant 5
> }
>
>
> ###lipid tail###
>
> colvar {
>    name        tail
>    width 0.1
>    lowerboundary -10.0
>    upperboundary 10.0
>    lowerWall -5.0
>    upperWall 5.0
>    lowerWallConstant 5
>    upperWallConstant 5
>    distanceZ {
>        main {
>           atomsFile tail_main.ref
>             atomsCol    B
>             atomsColValue      1.0
>         }
>        ref {
>           dummyAtom ( 0.000, 0.000, 0.000 )
>         }
>          axis (0.0, 0.0, 1.0)
>    }
>  }
>
> Can anyone give me some suggestions here, I am really confused.  Thanks a lot!
>
>
> Emilia
>
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:47 CST