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
--
========================================
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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