[gmx-users] reg explicit and implicit solvent model

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear justin,
> Thank you for your previous reply
>                   what is explicit and implicit solvent model ?

Please use Google and/or your favorite simulation textbook.

>                       In gromacs  Normally which one is implemented and 
> used bydefault

There is no default.  You make the choice based on how you set up your system.

> I want to use explicit solvent model in order to account electrostatic 
> effect of ions  on H-bonding
> I mean here i am studying the effect of ionic strength on h-bonding of 
> my protein for that Which tool of gromacs can i use to get proper result

Start with g_hbond.  Beyond that, read the manual (Appendix D) for the 
capabilities of all the different programs.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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