Hi,
Try the following two step processing:
#### first ptraj run ####
trajin tic_md_1.mdcrd 1 10000
unwrap :1-436
image center :* familiar com :1-436
trajout temp.mdcrd
#### second ptraj run ####
reference tic.rst7
trajin temp.mdcrd 1 10000 200
rms reference out tic_md_rmsd_new.dat .CA,C,N
On Tue, May 10, 2011 at 12:09 PM, Alex Rodriguez <alexdepremia.gmail.com>wrote:
> Hello everybody,
>
> I'm having what seems to be a system imaging problem, and I'm not able to
> solve it.
>
> I'm performing a pretty long trajectory (70 ns) on a protein dimer with two
> non-protein substrates (4 solute molecules). I performed it with PME in a
> cubic box and with iwrap=1.
>
> The question, is that when performing the rmsd analysis, it leads to
> unrealistic results. As recommended in the list, I tried to center the
> image. The ptraj script that I employed is:
>
> reference tic.rst7
> trajin tic_md_1.mdcrd 1 10000 200
> center :1-217 mass origin
> image origin center
> center :1-434 mass origin
> image origin center
> center :1-435 mass
> image origin center
> center :1-436 mass
> image origin center
> rms reference out tic_md_rmsd_new.dat .CA,C,N
>
> And the output is attached.
>
> Any suggestion?
>
> Thanks in advance
>
> Alex
>
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>
--
Best,
InSuk Joung
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Received on Tue May 10 2011 - 10:00:05 PDT
