Thank you Justin..
>> Is these alternative process is right or totally wrong..??? >> >> > Using the checkpoint in this instance is wrong. The only checkpoint you > have accessible to you at that point is from the end of the pulling > simulation and corresponds to the final state of the system. Applying > these velocities to the intermediate configurations along the reaction > coordinate is likely to do weird and unreliable things to the trajectory. > It is more robust to run NPT and then data collection, or as I said > before, proceed immediately to a continuous data collection (with gen_vel = > yes!) and discard the initial few ns of data as equilibration. In theory, > this procedure is no different than any other simulation that one conducts. > > > Check point file has velocity of the last co-ordinates and we are using middle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reason??? Thank you in advance... With Best Wishes, Rama David.
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