hello
I have done a 50ns MD simulation production run on three different protein-peptide complexes. unfortunately, I am getting quite a high RMSD in all of them. I tried many things but couldn't get a conclusion out of it. although all three protein complexes are moving out from the simulation box in the last frame only. I tried recentering by -pbc nojump and -pbc whole but it doesn't fix my problem.
please help
Thank you
Hi,
How many times have you equilibrate your system?
50ns is short if possible increase the production run.
If the problem is pbc then use any other program like:
Cpptraj
VMD
https://docs.mdanalysis.org/stable/documentation_pages/transformations/nojump.html
Regards,
Aashish
Compare your results with you control protein...... If the complex is having lesser fluctuations than the control then its ok....
Again, increase your simulation time if possible (at least 100ns) as initial phases of the simulation time, system tends to reach equilibrium.....
Regards
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