On Mon, Feb 17, 2025, TUSHAR GUPTA via AMBER wrote:
>My work includes working on the protein aptamer complex where i am working on the 3HSB protein complex.
>Please provide your valuable feedback and suggestion for solution
I've tried to do this twice before (see below). Maybe others on this list
can phrase things in a different manner, or provide suggestions of their
own.
....dac
>>Basically, you are getting different results from CPU and GPU. To start
>>debugging, set up a short simulation (say 20 steps, with ntpr=1) and run
>>twice, once with pmemd (not sander) and again with pmemd.cuda_DPFP. Look
>>carefully at the two outputs to see what you can find.
>
>The hope is that these short runs may help identify the reason for the
>difference between pmemd and pmemd.cuda. I'm guessing that we are going to
>need to see your files, but you should do this test yourself first.
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Received on Mon Feb 17 2025 - 20:00:02 PST
