Re: Re: Unfavorable anti conformation after GLUP patching?

From: Sébastien Légaré (
Date: Sat Apr 18 2009 - 21:43:22 CDT

Hi Sebastian

> How can one measure \Delta_G(gradually increase/decrease)?
> Instead of aiming for option (a), I would do (b) with the PMF module of
> NAMD >=2.6 and its "growth" command. Thus, you calculate \Delta_G by
> slowly raising the force constant on the dihedral. Don't ask me what
> "slow" means :-), usually people look at convergence behaviors. In
> another case, I raised a positional restraint force constant on a single
> atom to 10kcal/mol within 1ns for a total system with ~100K atoms (PMF
> script attached).

Thanks. I see the idea and I will try it. There is a "dihe pmf" in urestraint.
They just don't talk about this the papers I referenced in the previous
messages. It will probably give a really small ΔG.


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