On Wed, Jul 8, 2015 at 5:31 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
> Dear all,
> i have simulate a organic molecule in 128 methanol in a cubic box of 21
> angstrom and after 60ns production , i want to use final coordinate for
> abinitio md, Therefore i load my trajectory in VMD to save last frame
> coordinates but after loading i saw that all the methanol molecules are too
> much far away from each other and their coordinates are out of box, for
> this i used another option given in Amber program such as ambpdb to save
> coordinates but it also show to much variable coordinates , specially in
> negative values. What is going wrong, Please help me in this regard.
>
This is natural -- you would expect individual solvent molecules to drift
out of the unit cell from which they started. But keep in mind that with
periodic boundary conditions, when a particle drifts out of a particular
unit cell, another of its periodic images drifts in on the opposite side.
This is simply a visualization artifact caused by the fact that we only
store the positions of *one* image of each particle (it's impossible to
store all infinity of them, obviously). You can use the "autoimage"
command in cpptraj to map everything back into a single unit cell if this
helps:
trajin your_trajectory
autoimage
trajout imaged_trajectory
Obviously change the names of the trajectory files to what you want.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 08 2015 - 06:30:03 PDT
