Hi,
To extract frames at a specific temperature you need to add the ‘remdtraj’
and ‘remdtrajtemp <T>’ keywords to the ‘trajin’ commands. See the manual
for full details - there is a whole subsection on REMD trajectory
processing I think.
-Dan
On Tue, Sep 29, 2020 at 3:27 AM Aravind R <aravindspg27.gmail.com> wrote:
> 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
>
> proceed?
>
>
>
> Regards,
>
> Aravind R
>
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Received on Tue Sep 29 2020 - 05:00:02 PDT
