Dear all,
I am a beginner in Amber and wanted to know if the equilibration step can
be done in multiple steps with decreasing the force constant.
I am working on DNA molecular dynamics simulation. Prior to equilibration,
I have done minimization and heating(from 0 to 300k with K=20 for 20ps).
When equilibrating the system with decreasing force constant (K1=20, K2=10,
K3=5, K4=1, and without constraints). During the starting of the second
step of equilibration (K2=10) temperature is shooting up to 700 K. After
that everything is going well. Should I continue or this can cause any
problem?
Thanks
Priyabrata Das
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Received on Mon Apr 01 2019 - 03:30:01 PDT
