normal add PME to Martini

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11 years 4 months ago #1227 by richor
add PME to Martini was created by richor
Dear all:
I want to simulate a protein with Na+, but the Martini doesn't consider the long range coulomb force.
This feature seems have some influence on my system,so I want to use the PME to reduce the affect.
Is there any one know something about how to add PME to Martini force field?

Any answer will be appreciated!

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11 years 4 months ago #1230 by djurre
Replied by djurre on topic add PME to Martini
If charges (like ions) are important in your system, you probably want to use polarizable water (Yesylevskyy, 2010, PLOS Comput. Biol.) This has been tested (to some extend) using PME (see paper).

Depending on what kind of interactions you're expecting the Na+ to have, you might also be interested in the Martini 2.2P force field, which we (hopefully) publish soon. Here the charged and polar amino acid side chains are modified, to better mimick the binding of opposite charges and polar interactions. The Martini 2.2 force field has been implemented in the martinize.py script.

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11 years 4 months ago #1239 by richor
Replied by richor on topic add PME to Martini
djurre:
Thank you so much .
I will accept your suggestion.

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11 years 4 months ago #1240 by richor
Replied by richor on topic add PME to Martini
Dear djurre:
Just another qustion.
What is the difference of Martini force field 2.2 and 2.2P?
"Improved Parameters For The Martini Coarse-Grained Protein Force Field", J. Chem. Theor.Comp., submitted, 2012.----Martini force filed 2.2
Polarizable water model for the coarse-grained Martini force field. PLoS Comp. Biol, 6:e1000810, 2010.
Martini force field 2.2P?
Does this match correct?

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11 years 4 months ago #1245 by djurre
Replied by djurre on topic add PME to Martini
The 2.2P forcefield is to be used with the polarizable water AND has some improved parameters for polar and charged amino acids. The polar residues (Asn, Gln, Thr, Ser) carry partial charges (the are now actual polar) and the charged residues have the charges not at the center of the bead but at a seperate dummpy bead.

If charged/polar residues are particular important in you system, you might want to try it. Else, stick with the normal Martini water with the 2.2 version.

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