>
> The key thing to remember here is that what you see with imaging and what
> is actually happening in the simulation can and often do look like
> different things due to imaging artifacts. When your original trajectory is
...
> re-imaging. If there still imaging artifacts after this you may need to
> choose a different anchor molecule (i.e. the molecule that will be centered
> and that all other molecules should be 'close' to) with the 'anchor'
> keyword (by default cpptraj chooses the first molecule). Also be aware that
> many commands in cpptraj (distance, watershell etc) are already
> 'image-aware', so re-imaging is not necessary for these commands.
The key is the anchor and getting the anchor in the right place to begin
with. From the description it sounds like the lipid bilayer is
translating; there is nothing to prevent this. What it will look like is
more water appearing on one side. You need to translate the "anchor" to
where you want it to be and then autoimage around this. However, this is
not trivial to do. If I could, I would RMS fit to the first frame the
anchor, but RMSd rotates the box so this will kill imaging. Ideally, I
would figure out how much in X,Y, and Z the anchor has moved and then
translate back or do an RMS fit without rotation (which I do not think is
possible at present...
--tec3
>
> Hope this helps,
>
> -Dan
>
>
> On Mon, Mar 10, 2014 at 8:18 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> > wrote:
>
> > Since I used "iwrap" command, I used "unwrap" command and reimaged the
> > trajectory using commands as below:
> >
> >
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > trajin ../$system-MD300-run0900.traj 1 100 5
> > trajin ../$system-MD300-run1000.traj 1 100 5
> >
> >
> > unwrap :1-1214
> > center :1-1214
> > image center
> > trajout abc.traj mdcrd
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >
> > Can anyone advice me how to treat this trajectory files? I wish I dont
> > want to repeat the simulations. It takes long time to simulation 300 ns.
> >
> > Hope I get solution to this problem.
> >
> > Thank you.
> >
> > Vijay Manickam Achari
> >
> > (Phd Student c/o Prof Rauzah Hashim)
> > Chemistry Department,
> > University of Malaya,
> > Malaysia
> > vjramana.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
\-/ Thomas E. Cheatham, III (Associate Professor)
-/- Department of Medicinal Chemistry, College of Pharmacy
/-\ University of Utah, 30 S 2000 E, SH 307, Salt Lake City, UT 84112
\-/
-/- tec3.utah.edu (801) 587-9652; FAX: (801) 585-6208
/-\ SKH-4914
http://www.chpc.utah.edu/~cheatham
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 10 2014 - 08:30:03 PDT
