Guest always escapes from the host.

[bowensha-tudelft]

May I please know how to add so-called "flat-well" restranints mentioned in paper https://pubs.acs.org/doi/10.1021/acs.jctc.5b00405? My hexanoate always escapes from beta-cyclodextrin at low \lamda_p and \lambda_c. I guess this is where the problem lies. Is it also a static restraint between two certain atoms?

[nhenriksen]

Not sure how familiar you are with (the somewhat complicated) AMBER style restraints .... If r2 and r3 and not equal, the range in between them will have zero restraint potential. For example, in the below restraaint there is a decreasing hamonic potential from 0.0 --> 4.1 Å, no potential between 4.1 <--> 7.1 Å, and an increasing harmonic potential from 7.1 --> 999 Å.
&rst iat= 3,109, r1= 0.0000, r2= 4.1, r3= 7.1, r4= 999.0000, rk2= 5.0000000, rk3= 5.0000000, &end

See 29.1.1 in Amber23 manual

[bowensha-tudelft]

Not sure how familiar you are with (the somewhat complicated) AMBER style restraints .... If r2 and r3 and not equal, the range in between them will have zero restraint potential. For example, in the below restraaint there is a decreasing hamonic potential from 0.0 --> 4.1 Å, no potential between 4.1 <--> 7.1 Å, and an increasing harmonic potential from 7.1 --> 999 Å. &rst iat= 3,109, r1= 0.0000, r2= 4.1, r3= 7.1, r4= 999.0000, rk2= 5.0000000, rk3= 5.0000000, &end

See 29.1.1 in Amber23 manual

Thank you for the very detailed information! I will check amber manual for this.