[gmx-users] MOVIE.pdb

[Justin Lemkul]

On 1/31/18 2:31 AM, Neha Gupta wrote:
> Hi Justin,
>
> I followed your protein-ligand complex tutorials to do the simulation.
>
> I intend to run the simulation for 50 ns.
>
> In the final md run section, can we modify the command like this
>
> nstxout-compressed  = 500000      ; write .xtc trajectory every 1000.0 ps
>
>
> You have written the .xtc trajectory every 10 ps.
>
> How would the above command change the o/p?

If you increase the number of steps between writing coordinates, you're 
saving fewer frames. With your setting, you're only saving every 1 ns, 
which is very infrequent. Make sure you save enough frames to see the 
behavior of interest and collect sufficient data.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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