Hello,
I am attempting to run my first MD simulation by following along with ambermd.org tutorial 1.4 Building Protein Systems in Explicit Solvent<
https://ambermd.org/tutorials/basic/tutorial7/index.php>, but I’m unable to obtain the same results.
>From what I can tell, my outputs are as expected until the addition of the truncated octahedron box of OPC water. The ‘solvateOct ramp OPCBox 10.0’ command yields substantially different numbers from the tutorial:
Scaling up box by a factor of 1.362725 to meet diagonal cut criterion
Solute vdw bounding box: 45.394 31.223 30.488
Total bounding box for atom centers: 72.648 72.648 72.648
(box expansion for 'iso' is 56.3%)
Solvent unit box: 18.865 18.478 19.006
Volume: 199737.607 A^3 (oct)
Total mass 106080.564 amu, Density 0.882 g/cc
Added 5341 residues.
I suspected the difference could be due to the Amber version used. I am performing this simulation using Amber20 (the newest version available on this HPC system<
https://docs.alliancecan.ca/wiki/AMBER>). When I instead use AmberTools21, I get different results (from tutorial and Amber20) with solvateOct. What perplexes me is that the tutorial’s webpage shows the same solvateOct outputtoday (Nov 10 2022) as it did back in Oct 24 2020 (accessed via the wayback machine) when Amber20 was the newest release.
Can anyone advice on which versions of Amber enable the tutorial to be reproduced (forgiving slight rounding differences?
Thank you,
Kerry
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Received on Thu Nov 10 2022 - 08:30:02 PST
