It does depend on what you are doing for the pmf. Is one of these
restraints going to be changed and used for umbrella sampling? If so,you
need it to be strong enough to hold the system at that value of reaction
coordinate, but no stronger since that usually narrows the distribution and
results in the need for closer spacing of windows. But again, I'm not sure
if this is related to what you are doing.
If you need 500 for the positional restraints, you can calculate that
moving 0.1 angstrom away from reference would take a few kcal/mol. That's a
pretty strong restraint. When force constants become very high, you need to
use smaller time steps to maintain the accuracy of the time integration
(and sometime just stability of the MD run). So I would avoid using higher
forces than you actually need.
On Jan 3, 2016 1:35 AM, "Rasha Alqus" <rasha.alqus.manchester.ac.uk> wrote:
> Dear amber users,
>
>
>
> I am running pmf calculation for my system, where i apply two forces the
> first one is on to keep my ligand at specific distance from graphene and
> the other force is applied to graphene ( position restraint)
>
> my question is dose using high values of force like 500 on position
> restrain on graphene effect my calculation.
>
>
>
> Thank you in advance for the help
>
>
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Received on Sun Jan 03 2016 - 05:30:03 PST
