Thanks very much for your help!
On Thu, Jan 20, 2011 at 11:56 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > 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 - 09:30:06 PST
