AMBER Archive (2007)

Subject: Re: AMBER: image command

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Jan 10 2007 - 00:25:48 CST

> I ran a MD simulation using a truncated octahedron box. Then I imaged the
> trajectory using the following input files for the ptraj command:
>
> trajin ../name_md1.mdcrd
> trajin ../name_md2.mdcrd
> trajout ../name.pdb pdb
> rms first out rms @P,O3',O5',C3',C4',C5'
> center :1-24
> image familiar
> go

The above script will center to the box center (boxx/2, boxy/2, boxz/2)
and then image (to the closest spherical shape).

> trajin ../name_md1.mdcrd
> trajin ../name_md2.mdcrd
> trajout ../name.pdb pdb
> rms first out rms @P,O3',O5',C3',C4',C5'
> center :1-24
> image origin center familiar
> go

This script will center to the box center, but image via the "origin"
(i.e. box center is assumed to locate at 0,0,0; this will leave the solute
(:1-24) at the edge of the box.

> The final trajectories show many overlap between water molecules.

This I do not understand; what waters are overlapping; or equivalently,
how are you seeing that the waters overlap? This should only happen if
the box information is incorrect (in the mdcrd files unless it was
overridden with the box command).

>
> So I tryied to use the IWRAP option in the MD run:
>
...
>
> However, at the beginning of the simulation, my molecule is placed outside
> the box and the center command of ptraj (please see below) doesn't modify
> the solute position.
>
> trajin ../name_md1.mdcrd
> trajin ../name_md2.mdcrd
> trajout ../PDB_traj/name_md_centre.pdb PDB
> center :1-24
> go

The center command above only shifts the relative position of the ENTIRE
box, i.e. it places the center of mass of residues 1-24 at the box center,
i.e. boxx/2, boxy/2, boxz/2.

The IWRAP in sander and image in ptraj are effectively equivalent in the
usage as per the first ptraj script you specified...

If you are still stuck, you can e-mail me directly (with the prmtop and
part of ../name_md1.mdcrd) and I can try to help decipher.

--tom

tec3 @ utah.edu

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