[gmx-users] simulation time vs side chain flexibility

MD refmac5 at gmail.com
Tue Feb 20 17:48:23 CET 2018

Hi Gromacs folks,

I am trying to tell if a mutation can cause some part of the protein
becoming more flexible. I started with the apo protein. I did two
simulations in parallel, with one wild type and one with a silico mutation.

After a 10 ns simulation I was able to tell some region of the protein is
more flexible based on the RMS chart. Since side chain flexibility is in
the range of 1 ns, I wonder if 10 ns simulation is convincing enough?



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