Hello,
As far as I know, there is no way to do this within the ntr=1 framework.
What I do (during initial minimization/equilibration of my system for
dynamics) is to run several short simulations (50-100ps length) with
subsequent decreasing positional restraint weights.
I will run minimization with a particular value (5 kcal/mol A^2), then run
dynamics with the same value.
I step down until I reach zero: (5, 4, 3, 2, 1, 0.5, 0/unrestrained/no
ntr=1 flag).
-Christina
On Fri, Jul 10, 2020 at 9:38 PM David Sáez <davidsaez.udec.cl> wrote:
> Dear Amber community, is there a way to slightly turn off positional
> restraints (ntr=1, restraint_wt) on a molecule?
>
> I though a line like
>
> &wt type='REST', istep1=0, istep2=100, value1=1.0, value2=0, &end
>
> could work, but as &wt is related to nmropt=1 I am not sure if it would
> also affect the keyword ntr=1.
>
> Thanks in advance,
>
> David.,
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>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Mon Jul 13 2020 - 06:00:05 PDT
