On Thu, Jan 20, 2011 at 11:47 AM, dhacademic <dhacademic.gmail.com> wrote:
> 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?
>
This is one way of doing it, but it's overkill in my opinion. You only need
to image if not every lipid is in the primary unit cell. However, if you
center and image around a single lipid molecule in the middle of your
bilayer, then chances are a large number of lipids around it will be
properly imaged into the correct unit cell. You do not then have to
individually center and image these. That's why I suggested visualizing
them after each time you centered and imaged.
For instance, suppose each lipid molecule is 1 residue, and residue 15 is in
the 'middle' of your bilayer, and your
center :15 mass origin
image origin center familiar
Then visualize your system. Now suppose that only a couple lipid molecules
are not properly imaged, let's say the first 2 and last 2 lipid residues in
each layer. Now you want to center around the lipids that are properly
imaged and image the rest.
center :4-33,38-67 mass origin
image origin center familiar
then visualize again, and see if everything's imaged properly.
I hope this helps clarify more.
Good luck!
Jason
> 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
> >
> _______________________________________________
> 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
Received on Thu Jan 20 2011 - 09:00:03 PST
