Hello,
I am trying to calculate free energy required to restrain a ligand.
So far, I have tried using TI implemented in Amber18, where I described the
unrestrained and restrained ligand in the same prmtop file and used a
lambda parameter to go from the unrestrained to the restrained state.
However, the dV/dlambda values which I got are close to zero.
I am currently considering running two separate MD simulations with and
without restraints and then using MBAR to estimate energies.
Is there any other way this can be done, particularly using TI ?
Thanks for your help,
Sukanya
-
Sukanya Sasmal
Postdoctoral Scholar
David Mobley Lab
UC Irvine
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Received on Thu Nov 29 2018 - 18:30:02 PST
