You can use the targeted md function for this. My opinion though is that
rmsd is a poor reaction coordinate. At low values it is reasonable but at
higher values it does not define a single region of space, and to get
converged data you need to sample all structures that have a specific rmsd
value. That can be very, very difficult.
On Dec 6, 2015 10:10 PM, "Srinivasaraghavan Kannan" <
ragav.journals.googlemail.com> wrote:
> Dear
>
> Can anyone tell me how to use /ΔD/_/rmsd / as order parameter(reaction
> coordinate) in umbrella sampling to compute PMF. There are publications
> (J. Phys. Chem. B, 2014, 118 (1), pp 134–143)(J. Am. Chem. Soc. 2005,
> 127, 6866– 6876) using this with amber package, but i don't know which
> module to apply.
>
> Thanks.
>
> Ragav
>
>
>
>
>
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Received on Mon Dec 07 2015 - 03:30:03 PST
