[gmx-users] Please provide some advice on my simulations
mark.j.abraham at gmail.com
Tue Jan 23 17:50:37 CET 2018
The code isn't designed to produce reproducible trajectories, and generally
you should not want that. See
should also consider the characteristic timescales of the thing you want to
observe. If an unexpected event has occurred once in two replicates each of
100ns then you have a clue that the simulation design needs to be much
longer - depends what you want to observe, of course.
On Tue, Jan 23, 2018 at 5:10 PM vijayakumar gosu <vijayakumargosu at gmail.com>
> Dear gromacs users,
> I have performed simulation for RNA bound protein complex (350000 atoms).
> however within 10ns i have observed unusual large movement of N-terminal
> region and shows interaction with dsRNA, which may not be possible, however
> I have run simulations for 100ns. In order to check the consistency i have
> run one more simulation with the same system setup and performed dynamics
> for 100 ns, I have not observed the N-terminal movement and interaction
> with dsRNA, which is what i was looking for. But i am bit confused here to
> come to conclusion, why my first simulations were bit different compared to
> the second simulations despite same number of water molecules, box and
> Please provide some suggestions.
> Thanks a lot in advance.
> Vijayakumar Gosu Ph.D
> Post Doctoral Fellow
> The Animal Genomics and Breeding Center
> Chonbuk National University
> Tel: +821073270537 <+82%2010-7327-0537>
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