VMD-L Mailing List
From: Massimiliano Porrini (mozz76_at_gmail.com)
Date: Mon Mar 03 2014 - 03:45:21 CST
Thanks a lot, very useful tips.
On 3 March 2014 07:06, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> 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>
> 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
> theQM-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
> 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
-- 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 France http://www.iecb.u-bordeaux.fr/ Emails: m.porrini_at_iecb.u-bordeaux.fr M.porrini_at_ed.ac.uk maxp_at_iesl.forth.gr mozz76_at_gmail.com