Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark

From: Dr. Anselm Horn <>
Date: Wed, 26 Jan 2022 12:15:06 +0100

Dear all,

I performed a quick test on that topic. Here is what I did.

First, I created modified top files of FactorIX in that way that the
five negative values in the section %FLAG DIHEDRAL_PERIODICITY were made
positive. Both simulation setups, NPT and NVE, from the Benchmark Suite
were used, but I extended the runtime (nstlim) by a factor of 10. Two
simulations for each system were run on two different GPUs (RTX3080,
A100) using Amber20 (with patches 1-8).
Afterwards, I processed the out files with process_mdout.perl to obtain
a list of ETOT values (summary.ETOT).

1, Binary trajectory and restart files were identical for the two
consecutive runs of the identical system on the same GPU type, as were
the summary.ETOT files. -> Simulations ran successfully, as expected.

2, Binary trajectory and restart files were not identical for the
systems with original and changed top files, as were the summary.ETOT
files. -> Modification of top files affected simulation.

3, Difference
The mean absolute differences between the runs were as follows (400 data
points, orig: original top file, corr: modified top file):

NPT orig vs. corr (A100): ca. 9700 kcal/mol
NPT orig va. corr (RTX3080):ca. 9800 kcal/mol
NVE orig vs. corr (A100): ca. 9900 kcal/mol
NVE orig va. corr (RTX3080):ca. 9900 kcal/mol

NPT-orig (A100 vs RTX3080): ca. 80 kcal/mol
NPT-corr (A100 vs RTX3080): ca. 70 kcal/mol
NVE-orig (A100 vs RTX3080): ca. 20 kcal/mol
NVE-corr (A100 vs RTX3080): ca. 10 kcal/mol

-> Modification of the top files yielded results in ETOT at least ca.
two orders of magnitude larger than differences in MD runs on different

=> Changing the sign in the section %FLAG DIHEDRAL_PERIODICITY seems to
be significant.

But I encourage others to do similar checks, or course!

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 25.01.2022 um 23:06 schrieb John Chodera:
> David et al.,
> Thanks so much for the quick response!
> On Mon, Jan 24, 2022 at 1:43 PM David A Case <> wrote:
> I think what John has found is one example of the twenty-year-old prmtop
>> file where this rule is not followed.
> I suspected this might be case, but wanted to make sure we weren't
> accidentally causing problems for Amber users with valid use cases!
> About the factor_IX benchmark: the first simple task (volunteers, please!)
>> would be to manually change the five negative entries to be positive, and
>> see
>> if the results change. If we are lucky, we can just update the prmtop
>> file.
> I'll give this a try!
> Thanks!
> Best,
> John
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Received on Wed Jan 26 2022 - 03:30:02 PST
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