Dear all,
I am new to running umbrella sampling simulations. I am trying to build the free energy profile for a base unstacking of a helix using umbrella sampling. I am using a 15 windows system with RC going from 4.0 to 7.75 Angstroms. I am expecting to see a state change at around 5.0 to 5.5 Angstroms. I am feeding the restart file of the previous window as the initial structure for the next window.
My questions are,
*
Do I need to minimize, heat and equilibrate the system at the start of each window even if I am using the restart file from the previous window?
*
How does the frequency of dumping RC data to the dumpave file affect the free energy profile?
I already ran some umbrella sampling simulations for the system, with differing simulations times per window and got very different results for free energy profile each time. (I did not carry out minimization,heat,equilbration in each window for these simulations. That may have been the issue.) I have attached them for reference (I have checked for convergence and that looks fine to me). Can anyone give me an idea about what's causing this issue? Thank you!
Best
Risi
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Received on Thu Jul 18 2024 - 12:00:02 PDT
