Dear Jason,
Thank you for your useful suggestion.
Regards
-GGsmith
On 7 March 2015 at 18:00, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Mar 7, 2015, at 6:22 AM, GG Smith <ggsmithibab.gmail.com> wrote:
> >
> > Dear Amber Users,
> >
> > Am trying a simulate a protein+nucleic acid complex. I would like to
> > restrain distance between atoms of interest at particular distance
> > geometry for few ns in production run itself (sought of guided
> > simulation) and then do a free simulation. But am not sure of the
> > force constant to use for restraining the atoms mentioned in list
> > rst.dist (in my case). Pls. find below my input files.
> >
> > I would like to know What is ideal range for 1) restraint_wt and 2)
> > rk2 and rk3. Request to offer your insights and see if am going right.
>
> Note that your “restraint_wt” is not doing anything in your simulation.
> It corresponds only to the positional restraints set with ntr=1. I usually
> use force constants between 1 and 10 for positional restraints. For the
> flat-well NMR restraints, the strengths of the force constants you should
> use depend on what you are trying to accomplish with them. Since you have
> a distance range that is unbiased, a larger force constant seems warranted
> for violations. So I would say it looks fine (but it’s obviously more
> important how it affects your simulation than what I think).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Sun Mar 08 2015 - 23:30:02 PDT
