[gmx-users] How To Turn Off Electrostatics Linearly in TI Simulations

[Michael Shirts]

> However, if I were to linearly decouple the Coulombic interactions, does
it mean I slowly reduce the cut-off for > Coulombic interaction to 0
angstroms?

No, it is reducing the contribution of q_i q_j energy terms in the atoms
being coupled to zero.


On Sun, Jul 13, 2014 at 10:59 PM, Yip Yew Mun <yipy0005 at gmail.com> wrote:

> I read the mdp options for sc-coul, and I understand that by setting to
> the default option, I’m not applying the soft core energy to the Coulomb
> interaction. However, if I were to linearly decouple the Coulombic
> interactions, does it mean I slowly reduce the cut-off for Coulombic
> interaction to 0 angstroms? If not, what is the technical action to execute
> in the mdp file?
>
> Thanks.
>
> On 7/13/14, 10:10 AM, Yip Yew Mun wrote:
> > Hi all, I?m planning to run thermodynamic integration (TI) simulations
> with a few lambda values. I read articles and found out that the one of the
> better ways to deal with these lambda simulations is:
> >
> > 1. Disable all electrostatics linearly.
> > 2. Disable LJ terms by soft core.
> >
> > Therefore, what I wish to ask is how do I disable electrostatics
> ?linearly? in the mdp files of these lambda values?
> >
>
> Linear decoupling of Coulombic interactions is the default behavior;
> please read
> the description of the options in the manual (sc-coul being the most
> directly
> relevant to this issue).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> Biological Chemistry
> School of Physical & Mathematical Sciences | Nanyang Technological
> University | Singapore 639798
> Tel: (+65) 97967803 | Email: yipy0010 at e.ntu.edu.sg | GMT+8h
>
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