[gmx-users] g_potential help

[rajat desikan]

Thank you!

On Tuesday, April 22, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/21/14, 5:11 PM, rajat desikan wrote:
>
>> Hi Justin,
>>
>> So different parts of my system in Z-direction should be scaled
>> differently, right? On a coarse level, aqueous part with a scaling of 80,
>> membrane with a scaling of 2? How do I correct for this? Can I take the
>> quantitative output for potential difference across a membrane in water
>> from g_potential literally?
>>
>>
> You don't need to scale anything.  The force field parameters for every
> biomolecular force field that I know of are based on epsilon_r = 1, i.e. no
> special alteration of vacuum permittivity.  The results, at face value,
> should be sufficient.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore