Hi Christina,
Thanks for your reply and for sharing your experience on this topic. I will
follow your advice,
David.
El lun., 13 jul. 2020 08:42, Christina Bergonzo <cbergonzo.gmail.com>
escribió:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
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Received on Mon Jul 13 2020 - 09:00:03 PDT
