[AMBER] Inconsistent results on TI with cpu vs gpu code

From: Giorgos Lambrinidis <lambrinidis.pharm.uoa.gr>
Date: Wed, 5 May 2021 20:42:58 +0300

I am running a TI simulation using the method of Thomas Steinbrecher and
Hannes H Loeffler

My system has a complex of protein+ligand embedded to lipid bilayer.
I ran the production of TI with CPU and GPU separately.

Using pmemd.cuda the results were:
dG sum for Complex: 6.4 dG sum for Ligand: 6.2 and ΔΔG=0.2

When I run the simulation using pmemd.MPI the results were
dG sum for Complex: 5.6 dG sum for Ligand: 6.3 and ΔΔG=-0.7

The difference is mostly on the complex while I was expecting to be in
ligands transforamtion because I used on cuda code the -AllowSmallBox flag
which was not the default choice.
This Inconsistency is normal? If yes I can trust only the cpu-code results
and the cuda-code can not be trusted?
Any suggestion would be appreciated.

Best Regards
Dr. George Lamprinidis

“Good judgement is the result of experience and experience the result of
bad judgement.”
― Mark Twain
Dr George Lambrinidis
Researcher & Laboratory Assistant Staff
School of Health Sciences
Faculty of Pharmacy
National & Kapodistrian University of Athens
tel:  +30 2107274304
      +30 2107274521
fax:  +30 2107274747
e-mail: lambrinidis.pharm.uoa.gr
Guest editor of the Special Issues:
"Recent Advances in Drug Design" in "Molecules"
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Received on Wed May 05 2021 - 11:00:02 PDT
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