Re: [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file

From: Bill Ross <>
Date: Sat, 12 Dec 2020 10:57:32 -0800

I'd copy/paste that abnormal termination with cuda, plus how you're
equilibrating (mdin files).

Possibly if you equilibrate on CPU for a little, it'll run on GPU.


On 12/12/20 10:46 AM, Amit Sharma (Asstt. Prof., MCARS) wrote:
> Hi,
> In an NVT simulation I want to keep the time step as 1fs and SHAKE on all
> bonds including hydrogen.
> Please clarify if this means keeping ntc = 3 & ntf = 3? Or, if ntc and ntf
> should be specified with some other values?
> When I run NVT using ntc=ntf=3, run using pmemd.cuda gets terminated
> abnormally. However, it works fine with sander, but it is too slow. Any
> suggestion if we can use cuda when ntc=ntf=3?
> Thanks,
> Amit
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Received on Sat Dec 12 2020 - 11:00:02 PST
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