Thanks for the response.
But I for pmemd.cuda hybrid prmtop file needed. I already generated two end
states prmtop files.
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
On Mon, 20 Oct, 2025, 8:04 pm Timothy Giese, <giese025.rutgers.edu> wrote:
> The valid options for sander are:
> ifmbar ! turn on/off
> bar_intervall ! output frequency
> bar_l_min ! the minimum lambda (often 0.0)
> bar_l_max ! the maximum lambda (often 1.0)
> bar_l_incr ! the increment between states
>
> Unlike pmemd, one currently cannot input arbitrary schedules — one is
> limited to uniform schedules.
>
> If you are trying to perform alchemical free energy (AFE) transformations
> involving softcore functions, I highly recommend using pmemd.cuda (not
> sander and not the cpu version of pmemd). All of the AFE developments in
> the past 5 years have been made to the pmemd cuda code, and the pmemd cpu
> version was never updated to reflect the enormous number of improvements,
> bug fixes, and additions. One would typically only use sander to calculate
> "bookend" corrections via the indirect method (transformations that change
> potential energy functions rather than the chemical identity of a
> molecule). For example, the free energy of replacing a MM potential with a
> QM/MM potential.
>
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Received on Mon Oct 20 2025 - 08:30:02 PDT
