Hello,
I am running an umbrella sampling simulation using "colvar" namelist
and COM_DISTANCE as the reaction coordinate to keep the distance constant
between two chains of my protein. I notice that this method only works when
I am using amber/18 and when I ran the exact same simulation(same input,
initial configurations and ...) on Amber/20 the protein will get unfolded
in an obviously wrong configuration and also the constrain distance is not
satisfied. I should also mention that in both cases I am using GPU. I was
wondering if there is anything that I need to change in Amber/20 to get
similar result or the Amber/20 is not good for running umbrella sampling.
Thanks,
Ramin
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Received on Sat Apr 17 2021 - 09:00:03 PDT
