jalemkul at vt.edu
Wed Jan 31 17:51:30 CET 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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