**From:** Giacomo Fiorin (*gfiorin_at_seas.upenn.edu*)

**Date:** Wed May 13 2009 - 16:38:56 CDT

**Next message:**Eduardo Cruz-Chu: "Re: peptides on surface"**Previous message:**Jerome Henin: "Re: collective variable space PMF, including biasing potential terms?"**In reply to:**Sebastian Stolzenberg: "collective variable space PMF, including biasing potential terms?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Sebastian, two answers:

1) We haven't yet found an example where one method has clear

advantages. The best method is the one that gives the best results in

your case, and you're the judge. There can be an advantage with

respect to methods like umbrella sampling, where you sample a big

interval that you impose from the start, not knowing what their

relevance would be in the free energy plot. ABF and metadynamics

start instead from the lowest free energy regions, and then work their

way up until the maximum free energy that you decide to sample (20

kcal/mol? 50?). Other than that, it's very hard to say something

general, regardless of the system size.

2) It depends whether your Tcl forces are applied on the same atoms

you want to compute the PMF on. For instance, if you apply them on a

dihedral and then compute the PMF, the effect should be trivial: the

new PMF would be a sum of the "regular" one and your biasing

potential.

Technically, ABF measures the average forces from the system acting on

the collective variables, and by the way NAMD is designed they do not

include the user-defined restraints. Metadynamics doesn't the forces

at all, but looks instead at the resulting histogram in the collective

variable space, so implicitly it does take your external potential

into account. Then, there are three cases:

1. tcl forces and PMF calculation on the same atoms: sum your biasing

potential to the ABF-derived PMF, or take the metadynamics one as it

is; or even better, just compute one "unperturbed" PMF with either

method and sum the different biasing potentials to it to obtained the

"perturbed" PMFs :-P

2. tcl forces applied only on a subset of the "PMF" atoms: in this

case, ABF would miss some of the forces, but not homogeneously and you

can't simply sum your bias to the PMF. Metadynamics may be more

appropriate in this case.

3. tcl forces applied on different atoms from the "PMF" ones: ABF and

metadynamics should give you the exact same PMFs (minus sampling

errors).

Giacomo

---- ----

Giacomo Fiorin

Center for Molecular Modeling at

University of Pennsylvania

231 S 34th Street, Philadelphia, PA 19104-6323

phone: (+1)-215-573-4773

fax: (+1)-215-573-6233

mobile: (+1)-267-324-7676

mail: giacomo.fiorin_<at>_gmail.com

web: http://www.cmm.upenn.edu/

---- ----

On Wed, May 13, 2009 at 3:48 PM, Sebastian Stolzenberg

<s.stolzenberg_at_gmail.com> wrote:

*> Dear All,
*

*>
*

*> as far as I understand (with NAMD 2.7b1), there are two ways I can measure
*

*> potential of mean forces in collective variable space: ABF and metadynamics.
*

*>
*

*> 1.)
*

*> For small systems like the alanine dipeptide, does one PMF method have any
*

*> performance advantages over the other?
*

*>
*

*> 2.)
*

*> Eventually, I want to add a few biasing dihedral energy terms and measure
*

*> the effect on its free energy surface.
*

*> Thus, I also need to include the biasing dihedral terms into the PMF
*

*> calculations.
*

*> One way to do this I see is using tclForces with the "addenergy" command
*

*> (adding the dihedral energy terms into the "MISC" bin).
*

*> Which method, ABF or metadynamics, takes into the account the MISC energies
*

*> for the PMF calculation?
*

*>
*

*> Thank you,
*

*> Best,
*

*> Sebasitan
*

*>
*

*>
*

**Next message:**Eduardo Cruz-Chu: "Re: peptides on surface"**Previous message:**Jerome Henin: "Re: collective variable space PMF, including biasing potential terms?"**In reply to:**Sebastian Stolzenberg: "collective variable space PMF, including biasing potential terms?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:52:48 CST
*