[gmx-users] g_potential help

[rajat desikan]

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?

Thanks,

On Monday, April 21, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/21/14, 9:58 AM, rajat desikan wrote:
>
>> Hi All,
>>
>> I have a membrane-protein-solvent system, and I want the potential across
>> the membrane in the direction of the membrane normal. I have 2 questions
>> in
>> that regard.
>>
>> 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water
>> interface and ~2 for the hydrophobic membrane core. g_potential returns
>> the
>> result for epsilon_r = 1. How can I incorporate this into the result?
>>
>>
> I'd venture a guess that the value of epsilon_r in the output is the same
> as the interpretation of epsilon_r in the .mdp file - it is the relative
> dielectric permittivity.  A value of 1 means don't scale anything; see
> previous discussions.
>
>  2) Default ng =1? Is the number of groups referring to the number of
>> charge
>> groups defined in the topology?
>>
>>
> No, that means the number of groups you want to analyze, just like g_rdf
> and other tools sometimes give the option of doing multiple analyses at the
> same time.
>
> -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