Re: [AMBER] Regarding restarting from RST files using pmemd.cuda

From: Akinpelu Olayinka <>
Date: Mon, 19 Aug 2019 13:39:03 +0000 (UTC)

The rst file from the previous simulation should be your next starting point for the next simulation in pmemd.cuda.
There is nothing to be worried about.
    On Monday, August 19, 2019, 02:23:16 PM GMT+2, Daniel Roe <> wrote:

On Mon, Aug 19, 2019 at 6:57 AM Midhun K Madhu <> wrote:
> My question is, is it fine to consider the restart file(.rst) generated at
> the end of the first step to start the next step using pmemd.cuda program?
> Will it be a continuous run? As there is another option of pmemd.cuda.DPFP
> which will give more accurate restart files, I am a bit concerned about the
> restart files generated using pmemd.cuda.

The (default NetCDF) restarts from pmemd.cuda are written with full
double precision, just like the restarts from CPU pmemd; there really
is no "more accurate" than that. Is there a specific reason you are
concerned about restart files from pmemd.cuda? Have you seen strange
behavior etc?

> Also, what is the difference between pmemd.cuda and pmemd.cuda.SPFP?

Typically the former is a soft link to the latter. The SPFP refers to
the single-precision/fixed-precision model - for more details see


> regards,
> --
> Ph.D Student
> Dept. of Biological Sciences
> IISER Bhopal
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Received on Mon Aug 19 2019 - 07:00:01 PDT
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