Re: [AMBER] REMD Trajectory Processing

From: Carlos Simmerling <>
Date: Tue, 29 Sep 2020 09:18:19 -0400

yes this will give you replica trajectories, which you would want to
analyze for continuous properties such as pathway. Follow Dan Roe's advice
to obtain temperature-specific data (which is discontinuous in cartesian
space but can be used to evaluate thermodynamic or ensemble properties).
Note that the "pathway" data will be discontinuous in temperature and
therefore should be interpreted with caution.

On Tue, Sep 29, 2020 at 3:27 AM Aravind R <> wrote:

> Dear Amberites,
> To understand the folding pathway of protein of interest, I performed REMD
> simulation as mentioned in
> I did this as 3 * 10 us simulations each starting from the last as per
> suggestions from Jason in
> 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
> proceed?
> Regards,
> Aravind R
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Received on Tue Sep 29 2020 - 06:30:02 PDT
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