From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 12 2018 - 12:11:41 CST
I think we need a little bit more information.
You said you have already run a full FEP simulation (presumably scanning
through multiple alchLambda values with runFEP?) and that these completed
normally. If that is true, you almost certainly should not have to change
any of the settings that you mention (indeed, changing rigidbonds and/or
the timestep would change the answer for the free energy).
What structure are you restarting from? FEP calculations are usually very
sensitive to the initial structure and how representative it is of the
target alchLambda ensemble. This is why the sequential lambda approach is
often desirable. However, minimizing and re-thermalizing from lambda = 0 or
1 to some other lambda in the middle should be possible and stable.
There is a tendency for NAMD users to "over-minimize" their structures.
Because of PBCs and how wrapping works in NAMD *this is not a good idea*.
If you need more than ~200 steps to get a suitable structure for dynamics,
then there is probably something wrong with your initial structure and you
are only wasting time. Slow heating is another option, but I've rarely
since cases where this is truly necessary. In my experience, starting over
at a temperature of 0 is often more unstable than something closer to 300 K--000000000000b77f8b057a7ba219--
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