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.

Max

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.
>
>
> http://books.google.com/books?id=UQa3O3z8t98C&pg=PA28&lpg=PA28&dq=charmm+parameters+charged+offset+0.2&source=bl&ots=I8NILz8tt9&sig=Lilh9ryIeu4kGo3Deg_7BvYLg9w&hl=en&sa=X&ei=uxkUU72eJoXXkQf0roDoBg&ved=0CCkQ6AEwAA#v=onepage&q=charmm%20parameters%20charged%20offset%200.2&f=false
>
> 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
> 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
> 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.
>
> Best,
> Max
>
> --
> 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
>
>
> 

-- 
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