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

From: David A Case via AMBER <>
Date: Sun, 5 Feb 2023 12:02:16 -0500

On Fri, Feb 03, 2023, Thomas Cheatham via AMBER wrote:
>> We are struggling to achieve comparable results when performing the same
>> alchemical free energy protocols using amber2020 versus amber2022 (our
>> 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)
>Never trust a single run. You likely need multiple replicates

The original post already indicated that 5 replicates had been made. But it
might be useful to know how different the individual runs are from the
averages shown above. That would give a bit of a clue about how much the
sampling errors might be.

The input file had a but of a funny comment:

   nstlim=700000,!5ns production run

nstlim shows a 0.7 ns run, but the comment says 5 ns. We don't know if you
made many such runs for each lamda value or not.

The key point (I think) is that amber20 and amber22 seem to be giving
different results. (The empirical results are so far from either Amber
results that I would set them aside for the moment.)

One other test: with the same restart file, and fixing the ig value, run
parallel short runs with Amber20 vs Amber22, printing every step (ntpr=1).
Do you see any differences between the two codes.

I'm cc-ing this to Taisung in case he has thoughts about whether any
defaults in Amber22 are different from those in Amber20. But carefully
compare an mdout file from the two programs (say with vimdiff or some other
editor that can look at two files at once.) Look at the output before the
first step with an eagle eye, to try to spot anything that might be relevant
difference between the two sets of runs.


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Received on Sun Feb 05 2023 - 09:30:03 PST
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