**From:** *asaffarhi_at_post.tau.ac.il*

**Date:** Fri Jan 20 2017 - 09:34:05 CST

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Dear NAMD Users

We would like to introduce a recently published article on calculation

of relative free energies.

http://www.sciencedirect.com/science/article/pii/S0010465516303411

The article includes a decoupling analysis in which the partition

functions of the transformed molecules are decomposed into two

partition functions. It enables to keep dihedral angle terms and

coupled bond angle terms at the separation point on, independently of

the function type, also when there is a bond junction at the

separation point between the shared and unshared submolecules. The

decoupling analysis is demonstrated in a relative solvation free

energy calculation of p-Cl and p-CH3 and the calculation is shown to

be more efficient since less terms are removed. In addition, it is

proved analytically that when capping the non-bonded potentials (soft

core technique) the integrated function (in TI) is monotonic (has

implications for robusteness). It is also shown mathematically that

when capping the non-bonded potentials and the two molecules are

simulated separately, the integrated function can be non-steep. It is

also explained how when the systems have rugged energy landscape they

can be equilibrated in the same sampling dimension.

Other important references there:

Ref. 34 (33), where it has been suggested to simulate the two

molecules separately and to cap the potential with accessible energies

of ~5kcal/mol (page 28, denoted by E_cutoff).

Ref. 35 where it has been suggested to remove terms only of the atoms

of the unshared submolecules (v1 abstract, v6 Fig. 7) and to cap

potential terms with accessible energies of 7kcal/mol (v1 Eq. (24)).

This reference has been split to the article on relative free energies

and the article on calculation of molecular free energies (Ref 38).

Ref. 38 which is about an exact calculation of molecular free energies

in a general environment. The calculations include the free energies

of bond stretching, bond angle, dihedral angle, bond junctions, and

complex structures. These free energies are also relevant for

restraints in binding.

Here is the link:

http://iopscience.iop.org/article/10.1088/1367-2630/18/2/023039/meta

Thank you for your attention,

Best regards,

Asaf

**Next message:**Douglas Houston: "ABF with alpha colvar?"**Previous message:**Marcelo C. R. Melo: "Re: QM-MM ORCA Charm++ error Could not find QM output file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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