On Wed, Apr 01, 2020, mohamed marzouk wrote:
>I did conventional molecular dynamic simulation many times, my question
>related to NPT ( equilibration step ) how can I remove the position
>restrain gradually?
>To be clear, If I started the NPT step by position restrain 500 and want
>to decrease after 1 nsec to 450 then 2 nsec 400 and so on.
Just to add to what has already been said: a position restraint of 500
is way too high. I generally start at 10, then move to 1, then to 0.1,
then to zero. Nothing magical about my choices, but part of the reason
that there is no automatic facility in Amber is because developers have
not felt a need to have one.
...dac
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Received on Wed Apr 01 2020 - 07:30:02 PDT
