[AMBER] issues with pmemd.cuda

From: Veenis, Andrew Jay <ajv6.psu.edu>
Date: Thu, 25 Apr 2019 15:11:46 +0000

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Hello,

I am using MD to study a RNA enzyme. When I equilibrate the system on CPUs at our university's cluster using pmemd.MPI, I get sound results where the enzyme's configuration remains close to that of the crystal structure it was based on. Upon using the identical input files (same md5sum values) to run the MD on our computer using pmemd.cuda, residue 4 changes from a southern to a northern pucker during NPT equilibration (see 09_npt_eq_pucker.dat). This conformational switch does not occur when the simulations are run using CPUs.

I am using a computer purchased from Exxact to run AMBER. Ross Walker had me run DPFP and SPFP tests and they gave no indication that there is anything wrong with the AMBER installation.

The system was minimized using CPUs. I have attached the relevant files to this email. Am I doing something wrong or is there a bug in the GPU code?

Thanks,

Drew
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Received on Thu Apr 25 2019 - 08:30:02 PDT
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