VMD-L Mailing List
From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Mar 03 2014 - 00:06:04 CST
While never made explicit in the most recent charmm papers, this (relatively) old book states that polar-neutral interactions are shifted by 0.2 A, charged by 0.1 A, and nonpolar by none.
That being said, it seems the modern recommendation is that the distance is hardly important anyway and should be weighted very lightly compared to the energies/dipole moment.
On Feb 28, 2014, at 6:18 AM, Massimiliano Porrini <mozz76_at_gmail.com> wrote:
> Hi all,
> I am optimising atomic charges (from water-interaction profile) of
> a cationic (+1) molecule with ffTK of VMD and I quote below
> what is stated at Pag. 2760, 1st column, of the related paper
> (C.G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, J.C. Gumbart
> J. Comput. Chem. 2013, DOI: 10.1002/jcc.23422.):
> To better approximate the bulk-phase, for polar target compounds the
> QM-optimized distances are shifted by an offset of -0.2 Angs and
> the interaction energies are scaled by 1.16 (for neutral molecules only),
> although both parameters can be adjusted by the user.
> Therefore, since the molecule I am parametrising is not neutral but a cation,
> I do not have to scale the interaction energies (that is Scale = 1.0).
> What is not clear to me, from the paper statement, is whether
> the QM-optimised distances do not need to be
> offset by -0.2 Angs (in case of non-neutral molecules) either.
> Thanks in advance.
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> Emails: m.porrini_at_iecb.u-bordeaux.fr