GROMACS modification: none
I am running two machines both with gmx 2020.3 , Linux Mint 19.x The ‘slower machine (A) is an AMD Ryzen 7, 12 core , 2x1080Ti and the other (B) an AMD Threadripper 32 core and 2x2080Ti both with 32 gig .Gromacs and Nvidia toolbox 11 were recently a compiled with the latest g++, gcc on both machines.
I copied all the files ( mpd, restraints, itp top etc ) of a model of 200 nylon molecules 650 atoms each from A to B . The itp was created with gmx x2top and charges were modified slightly to bring total charge for all 200 molecules < 0.01 A surface was created in packmol ` 300 X 700 X 50 A which condenses down to 300 x39,3.4 on system A. with x constraints on the end atoms.
The model runs nicely on A, but not on B. I cannot get the model to even minimize - well it converges to > +10e8. If I use 1-5 molecules minimization reaches ~ -1. In contrast ,on A, minimization = ~ - 6e5 for all 200 molecules.
A bond rotation error appears in B under all conditions in nvt, and I’ve tried to use shake as opposed to Lincs to get to an equilibrium situation. On A the gmx selects ntomp =4 and ntmpi =4 ( other settings work as well ) on B I’ve adjusted these parameters to as low as 1 each and have tried as few as 10 molecules during nvt but the links, and many #steps appear . The errors appear with and without constraints which to apparently cross domain boundaries. I have tried adjusting cutoffs and grid spacings.
It turns out that none of the models - so far tried -that were made and ran on gromacs 2020.1 on system B as recently as a few weeks ago, now run Other cuda based programs ( Maestro, vmd ) do run normally. I’ve several hundred models that were created and ran on B, so I do not believe its the hardware.
This information is probably insufficient to provide solid suggestions ( please do if you know what is going on ) other than perhaps to comment on ‘typical’ differences between the older A and the middle age B, but may be sufficient to ask me for the proper info.