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

[vijayakumar gosu]

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