Re: [AMBER] image for lipid/water system

From: Jason Swails <>
Date: Thu, 20 Jan 2011 11:05:01 -0500

Did you use iwrap=1? If so, you'll have different lipid molecules
potentially wrapped all over the place, and it may not work to try and
center an entire layer (since it may be likely that parts of each layer may
need to be dragged into the center cell).

Try doing this in steps (it may take awhile). Choose a lipid molecule (I
don't know how many residues are in an individual lipid *molecule* -- you
can check the ATOMS_PER_MOLECULE section of the prmtop file) in the middle
of the bilayer (in one layer!) and center/image around that residue (using
familiar if you are using a truncated octahedral cell). Use the same
center/image commands you used in your examples below.

Then visualize the trajectory and center/image around the subset of the
bilayer that appears to be properly placed in the unit cell you're looking

If you recursively continue the above sequence of steps, you should
eventually arrive at what you're aiming for. Note, however, that this is
purely cosmetic and has no effect on your simulation.

Good luck!

On Thu, Jan 20, 2011 at 10:21 AM, dhacademic <> wrote:

> Hi amber users,
> I have a ptraj image problem after I have checked the previous archive of
> amber mail-list.
> My system is a small molecule (resid: 1) merged in lipid bilayer (resid:
> 2-69, in which 2-35 is one layer, and 36-69 is another layer) in
> rectangular
> parallelepiped water box. In the z-direction, the original organization of
> each layer is "W1--L1--L2--W2", where "W" means water and "L1 (or L2)"
> means
> one layer of lipid. I have tried different protocols to do the image.
> However, sometimes I can find "L2--W2--W1--L1" organization of the system
> in
> the whole trajectory.
> (1)
> trajin mdcrd
> center :1-69 mass origin
> image origin center familiar
> trajout newtraj netcdf
> ****
> (2)
> trajin mdcrd
> center :2-35 mass origin
> image origin center familiar
> center :1-69 mass origin
> image origin center familiar
> trajout newtraj netcdf
> Can anyone help to figure out the problem? Thanks in advance.
> Best,
> Hao
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jan 20 2011 - 08:30:10 PST
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