[gmx-users] Regarding soft-core potential

bipin singh bipinelmat at gmail.com
Tue Nov 26 16:22:40 CET 2013


Thanks for the clarification Dr. Justin.

Now it is clear to me.


On Tue, Nov 26, 2013 at 8:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Tue, Nov 26, 2013 at 9:56 AM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > Thanks for the reply Dr. Justin.
> >
> > Then is it not contrasting to the below statement, mentioned in online
> > manual ?
> >
> > "the soft-core alpha parameter, a value of 0 results in linear
> > interpolation of the LJ and Coulomb interactions"
> >
> >
> No, that's not inconsistent. If sc_alpha > 0, then scale LJ with soft-core
> and Coulomb linearly. If sc_alpha = 0, scale both LJ and Coulomb linearly.
>
> -Justin
>
>
> >
> > On Tue, Nov 26, 2013 at 6:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > > On Tue, Nov 26, 2013 at 7:52 AM, bipin singh <bipinelmat at gmail.com>
> > wrote:
> > >
> > > > Hello,
> > > >
> > > > Below is the text taken from the page number 97 of Gromacs 4.6.4
> > manual:
> > > >
> > > > "When soft core potentials are selected *(by setting sc-alpha ¿ 0)*,
> > and
> > > > the Coulomb and Lennard-Jones potentials are turned on or off
> > > sequentially,
> > > > then the Coulombic interaction is turned off linearly, rather than
> > using
> > > > soft core interactions, which should be less statistically noisy in
> > most
> > > > cases".
> > > >
> > > > *Doubt:*
> > > >
> > > >
> > > >
> > > >
> > > > *sc-alpha ¿ 0 is actually sc-alpha=0 *
> > > > Am I right ?
> > > >
> > > >
> > > No. The bogus character should indicate "not equal to."
> > >
> > > -Justin
> > >
> > > --
> > >
> > > ==========================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > 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
> > >
> > >
> > > ==========================================
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> >
> >
> > *-----------------------Thanks and Regards,Bipin Singh*
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>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
>
> ==========================================
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-- 


*-----------------------Thanks and Regards,Bipin Singh*


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