On Mon, 2014-03-10 at 14:18 +0000, Vijay Manickam Achari wrote:
> I have simulated bilayer in water. There are 128 lipid in total and
> around 600 water molecules on top and bottom of the lipid bilayer.
>
> Up to about 50 to 60 ns the trajectory works fine. Then I find the
> water molecules shift to one layer more than the other layer.
> After that I also notice the layers in the bilayer shift upside down.
> The water molecules become in the center and the tails of each bilayer
> pointing upward and bottom of the bilayer.
This is just an imaging artifact, as it seems that you suspected.
>
> I used mdinput as below:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Production 300ns constant pressure & zero surface tension
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntt=2, temp0=355.0,
> ntxo=1, iwrap=1, nscm=5000,
> ntb=2, pres0=1.0,
> ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,
> ntc=2, ntf=2,
> nstlim=100000, dt=0.002,
> ntpr=100, ntwr=-50000, ntwx=1000, ntwe=500,
> cut=10.0, ioutfm=1
> /
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> Since I used "iwrap" command, I used "unwrap" command and reimaged the
> trajectory using commands as below:
The "unwrap" command does nothing here since the 'reimaging' simply
reverses the unwrap action. [1] Since the 'unwrap' command seems to be
computationally demanding, I suggest getting rid of it.
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> trajin ../$system-MD300-run0900.traj 1 100 5
> trajin ../$system-MD300-run1000.traj 1 100 5
>
>
> unwrap :1-1214
> center :1-1214
> image center
You want "image origin" here. The "center" command sets the origin to
the center of geometry (or mass) of the mask. The "center" keyword in
the image command uses the center of mass of each molecule when imaging
instead of the first atom. I typically use "image origin center"
myself.
> trajout abc.traj mdcrd
I'd suggest using NetCDF as a format -- it's better in almost every way
(higher precision, much smaller file, and harder to corrupt).
In general, if you make sure that your analyses use the minimum image
convention when computing distances (as cpptraj does), it doesn't really
matter if your trajectory is not imaged the way you like it.
If you want the bilayer to 'look nice', then you need to define a box
center that will roughly correspond to the middle of the bilayer. The
image command will then grab all of the periodic images that are closest
to that point. If your bilayer extends to the sides of the box (as I
suspect it does), then you can simply center the system on an atom that
resides at the very end of a _single_ lipid tail. Try this:
======
trajin your_trajectory
center :<RESIDUE>.<ATOM>
image origin center
trajout abc.nc netcdf
======
You'll need to replace <RESIDUE> with the number of a residue that
represents the tail of one of your bilayer lipids. <ATOM> is the atom
name of the atom at the end of the lipid chain.
I think (and hope) this will work, but I've never actually run any
bilayer simulations.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 10 2014 - 08:00:04 PDT
