it depends on what you want to learn. for the kinetics, such as diffusion,
you are correct that you want the unimaged trajectory. for information about
whether water contacts a certain residue, then you want the imaged.
trajectory.
check the archives for details on imaging in ptraj, there are many examples.
On Fri, Feb 5, 2010 at 5:25 AM, Shaikh Abdul R S Ramaju <smasarsr.nus.edu.sg
> wrote:
> Dear Amber Users,
>
>
>
> I am analyzing the MD trajectory of Amber. I would like to calculate how
> many atoms of solvent molecules are in contact with each amino acid
> residue. For this reason I wrote a small Tcl script in VMD which can
> calculate contact of each residue with solvent molecules within 3.5 Ang.
>
>
>
> My question is I did NPT MD in Amber 10. In trajectory solvent molecules
> gets spread out in the space outside the box. When I do reimaging the
> atoms are placed back in the box. I am not sure which trajectory should
> I take to calculate the contact of solvent molecule.
>
>
>
> Is it that while reimaging the trajectory, the dynamics of motion is
> affect. I mean if in the original simulation the atoms flying around all
> the places under the spell of forcefield; won't the forces, and energies
> would be different, if I put them artificially in the box, while
> reimaging?
>
>
>
> Hope to hear from Amber users.
>
>
>
> Thanks a lot
>
>
>
> Abdul Rajjak
>
>
>
>
>
>
>
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Received on Fri Feb 05 2010 - 03:30:03 PST
