[gmx-users] Please provide some advice on my simulations

Mark Abraham 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
http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
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
> parameters.
> Please provide some suggestions.
> Thanks a lot in advance.
> Best,
> 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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