Read the AmberTools manual. Ptraj (& cpptraj) can read in trajectory files
and calculate RMSD.
Marc
PS are you not doing NVT in your first equilibration / heating step?
On 25 Jan 2012 10:45, "Atila Petrosian" <atila.petrosian.gmail.com> wrote:
> Dear amber users
>
> I did md simulation of protein as follows:
>
> 1) minimization
>
> 2) 200 ps equilibration (NPT)
>
> 3) 300 ps equilibration (NPT)
>
> 4) 1000 ps production run (NPT)
>
> In analysis step, I want to obtain RMSD in all of the simulation time
> (200+300+1000 = 1500 ps)
>
> how to do that?
>
> any help will highly appreciated.
>
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Received on Wed Jan 25 2012 - 03:00:04 PST
