can you provide your input file md1.in?
it may be that your ntwx is not set to output snapshots to the trajectory
file.
On Wed, Jan 6, 2021 at 7:58 AM K Jan <10dunajkr.gmail.com> wrote:
> Dear all amber users
>
>
> I have been simulating a molecule on Amber and I was wondering whether I
> could ask you a question as I am unsure of how to visualize my molecule
> with the output files that I have received from my sander code.
>
> I`ve completed analysis on the molecule by calculating the density, volume,
> pressure , radius of gyration and the Root Mean Square Deviation.
>
> I would like to use vmd to view the molecule at the different times of the
> simulation ( simulation lasted 80 picoseconds , and it was completed in
> steps of 10ps) . However, I don`t have any trajectory output files so I am
> not sure how to do this.
>
> This is my sander code:
>
> sander -O -i md1.in -o md1KCL.out -inf md1KCL.inf -c lr16wKCL.k.minw2 -ref
> lr16wKCL.k.minw2 -r lr16wKCL.k.md1 -p lr16wKCL.k.top -x lr16wKCL.k.md1.x -e
> lr16wKCL.md1.ene &
>
> and the output files I get are:
>
> lr16wKCL.k.md1, md1KCL.inf and md1KCL.out
>
>
> I have also tried running the code by using lr16KCL.k.nc after -x but this
> doesn’t work either.
>
> I need lr16wKCL.k.md1.x in order to view the molecule in the vmd but for
> some reason this code doesn’t output this trajectory file.
>
> Unless, does the lr16wKCL.k.md1 output file contain the trajectory and can
> I use this in lieu of the explicit trajectory file ?
>
>
> many thanks,
>
>
> Kris J Duna
>
>
> --
> null
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Received on Wed Jan 06 2021 - 06:30:05 PST
