[AMBER] REMD Trajectory Processing

From: Aravind R <aravindspg27.gmail.com>
Date: Tue, 29 Sep 2020 12:55:32 +0530

Dear Amberites,
To understand the folding pathway of protein of interest, I performed REMD
simulation as mentioned in https://pubs.acs.org/doi/abs/10.1021/ja5032776.
I did this as 3 * 10 us simulations each starting from the last as per
suggestions from Jason in archive.ambermd.org/201403/0529.html.
Now, to get a Replica trajectory and temperature trajectory for the entire
simulation, can I concatenate the trajectories from the 3 simulations using
trajin and trajout like the following?

parm Sys_Prep/d1.prmtop
trajin Prod_0us-10us/remd.mdcrd.001
trajin Prod_10us-20us/remd.mdcrd.001
trajin Prod_20us-30us/remd.mdcrd.001
trajout Analysis/remd.mdcrd.001

I ask this because REMD trajectories are bit different from the usual amber
trajectories and therefore does it make sense to do so. Can I do this for
all the replicas before I continue with the analysis? If not, how should I

Aravind R
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Received on Tue Sep 29 2020 - 00:30:02 PDT
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