[gmx-users] reg electrostatics

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear justin Thank you for previous patient reply
>   
>                       To study the salt effect  (ionc strength) on 
> H-bonding of protein
> Which option of Electrstatics is best either PME or Cut-off ?
> Because when i read one recent  articles They used Cut-off option I 
> Think PME is recent option

Plain cutoffs are archaic and lead to bad artifacts.  PME is probably the best 
method overall.

>  2) which one is best Water model TIP OR SPC WATER  MODEL  to study the 
> ionic strength.?
> 

The choice of water model depends on the chosen force field.  Some combinations 
perform better than others.  You need to do your homework here and make an 
appropriate choice.  There is ample literature on this topic.

> 3) which one is best( either implicit or explicit) water model to study 
> the effect of electrostatic interaction on H-bonding of protein?

You can't (easily) include explicit ions in an implicit solvent simulation. 
Explicit is probably the easiest route.

-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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