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
>
>
>
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