Thanks for the reply.
Actually I specified "iwrap=1" in my input. However, the molecules
(especially water) in the trajectory do not be wrapped into a primary box.
It is strange. So I tried post-processing with ptraj.
I have checked the prmtop file, in which one lipid molecule is a residue. Do
you mean that I need to center/image each individual lipids in the following
way, if the resid of lipid begins with n and there are m of them?
trajin mdcrd
center :n mass origin
image origin center familiar
center :(n+1) mass origin
image origin center familiar
center :(n+2) mass origin
image origin center familiar
...
center :(n+m) mass origin
image origin center familiar
trajout newtraj netcdf
On Thu, Jan 20, 2011 at 11:05 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> for.
>
> 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!
> Jason
>
> On Thu, Jan 20, 2011 at 10:21 AM, dhacademic <dhacademic.gmail.com> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 20 2011 - 09:00:02 PST
