GROMACS version: 2018.8
GROMACS modification: No
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I have performed a CG MD for a dimeric protein upto 4 microseconds. Now, I want to generate the AA gro/pdb from the CG trajectory. I have performed a cluster analysis to obtain a average structure from the CG trajectory. Regarding this I have the following questions:
Is it better to run replicates of the CG MD for accuracy?
While backmapping, will a 100 ns relaxation simulation is enough from a average structure from CG MD ?
Do I have to run replicates of the relaxation simulation as well?