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
behavior...
Thank you!
Michael Kim and Skanda Sastry
Below is our production script at one of the lambdas:
Explicit solvent constant volume production
&cntrl
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
dt=0.001,
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
"wra
pped" into a primary box.
ioutfm=1, !netcdf trajectory
ntr=1,!positional restraint
restraintmask='.CA,C,N&:1-16',
restraint_wt=1.0,
icfe = 1, ifsc = 1,
logdvdl = 1,
timask1='.6557,6558,6559,6560,6561,6562,6563,6564,6565,6566,6567,6568,6569,657
0,6571,6572,6573',
timask2='.8450,8451,8452,8453,8454,8455,8456,8457,8458,8459',
scmask1='.6557,6558,6559,6560,6561,6562,6563,6564,6565,6566,6567,6568,6569,657
0,6571,6572,6573',
scmask2='.8450,8451,8452,8453,8454,8455,8456,8457,8458,8459',
clambda = 0.43738,
/
&wt TYPE='END' /
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Received on Fri Feb 03 2023 - 18:30:03 PST
