Dear Lin,
Thanks so much for your kind help.
I use the following script to combine the 3 trajectories:
trajin nowat-com100ns-run-1.nc 1 last 50
trajin nowat-com100ns-run-2.nc 1 last 50
trajin nowat-com100ns-run-3.nc 1 last 50
trajout nowat-com100ns-combined.nc nobox
EOF
However, when I calculated the RMSD using the combined trajectory, the RMSD
plot seems weird.
I supposed that the cpptraj process using the script above was adding one
trajectory to another one,
so the combined trajectory become 300 ns long. This is not I want.
What I want when combining those nc files is the final nc file with 100 ns
long, not 300 ns.
Please let me know how to to that.
Forgive me if my Englis is poor.
Best regards,
Nada afiva
Pada tanggal Sel, 8 Sep 2020 pukul 08.23 Song, Lin <
songlin3.chemistry.msu.edu> menulis:
> Hi,
>
> You can use cpptraj of AmberTools to combine them:
> http://ambermd.org/tutorials/analysis/tutorial0/index.htm
>
> Best,
> Lin
>
> On Sep 7, 2020, at 7:59 PM, Nada Afiva <nadaafiva.gmail.com<mailto:
> nadaafiva.gmail.com>> wrote:
>
> Dear Amber,
> I run 100 ns MD and then I repeated it 2 times, so I have 3 trajectories
> for the same system.
> Now I want to combine the 3 trajectories into one single trajectory and I
> will use the single combined trajectory
> to calculate the RMSD ad other analyses.
> Please let me know how to combine the 3 trajectories into one single
> trajectory.
> Thank you.
>
> Best regards,
> Nadaafiva
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Received on Mon Sep 07 2020 - 19:00:02 PDT
