[gmx-users] reg explicit and implicit solvent model

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 13 17:12:43 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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