[AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc

From: Michael T Kim via AMBER <amber.ambermd.org>
Date: Fri, 3 Feb 2023 18:01:14 -0800

Hi all,

We are struggling to achieve comparable results when performing the same
alchemical free energy protocols using amber2020 versus amber2022 (our
results using amber2020 are more accurate compared to empirical
benchmarks). Caveat: while we perform the exact same input scripts and also
perform five replicates, we do use random seeds at the moment and have not
yet tested amber2020 vs amber2022 using the exact same seeds (we plan to
try this in the coming weeks).

below results are ddG, expressed in kcal/mol
system1: 0.71 (amber20), -0.23 (amber22), 1.15 (empirical)
system2: 0.55 (amber20), -0.17 (amber22), 0.83 (empirical)
system3: 2.35 (amber20), -0.05 (amber22), 3.15 (empirical)
system4: 3.96 (amber20), 1.29 (amber22), 5.59 (empirical)
system5: 2.58 (amber20), 3.39 (amber22), 5.82 (empirical)

Our main question is: have defaults changed between amber2020 and amber2022
that would affect alchemical free energy calculations (thermodynamic
integration)? We've included our lambda_production script below in case
something is incompatible with amber2022. We've compared amber2020 and
amber2022 manuals but did not find anything that would explain this

Thank you!
Michael Kim and Skanda Sastry

Below is our production script at one of the lambdas:

Explicit solvent constant volume production
  imin=0, !minimization off
  irest=1,ntx=5, !read coordinates,velocities
  ntpr=25000, !energy information in mdout
  ntwx=25000, !coordinates will be written to trajectory
  ntwr=25000, !coordinates will be written to trajectory
  nstlim=700000,!5ns production run
  ntt=3, !langevin dynamics
  gamma_ln=2.0, !collison frequency
  ig=-1,!random number generator
  ntc=1, !bonds involving hydrogen are not constrained
  ntf=1, !bond interactions involving H-atoms included
  cut=8, !nonbonded cutoff
  ntb=1, !constant volume
  temp0=300.0, !final temperature
  iwrap=1, !coordinates written to the restart and trajectory files will be
pped" into a primary box.
  ioutfm=1, !netcdf trajectory

  ntr=1,!positional restraint

  icfe = 1, ifsc = 1,
  logdvdl = 1,


  clambda = 0.43738,
 &wt TYPE='END' /
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Received on Fri Feb 03 2023 - 18:30:03 PST
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