I have run a regular MD on the same cyclic peptide and it runs fine and I
can do all visualisations and stuff. However when I generate the REMD
trajectories using the same structure, VMD gives the error of cannot load
trajectory.
Thanks
Suchetana
On Sun, Jun 26, 2022 at 12:58 PM David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Jun 26, 2022, Suchetana Gupta via AMBER wrote:
>
> >Is there any updated tutorial for running REMD simulations? I am trying to
> >do REMD simulations for cyclic peptides using Amber20. I have followed the
> >tutorial...
> >Somehow, I am unable to visualise the trajectory after following these
> >steps. The trajectory does not load in VMD. Any solution for it?
>
> There should be no particular connection between using REMD, and having
> your
> system be a cyclic peptide.
>
> 1. does your system run OK without REMD, and can you visualize the
> trajectories?
>
> 2. What is the exact error message you get in VMD? At what stage of the
> process?
>
> ...thx...dac
>
>
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Received on Thu Aug 04 2022 - 13:33:25 PDT
