> 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 Sat Mar 07 2015 - 05:00:03 PST
