From: doty alexiou (doty_alexiou_at_hotmail.com)
Date: Tue Jul 06 2010 - 06:22:30 CDT
Hello.I am using the residue-based-CG method in NAMD,using the based on Marrink's force field,extended to proteins.I have read the papers where this method is used to simulate nanodiscs etc.I concluded that this method takes into consideration the hydrophobic effect too, although 4 water molecules makes just 1 CG-bead.I am trying to simulate protein-protein interaction between two molecules where hydrophobic effect plays an important role.I have also implemented extra tcl-forces in order to keep the tertiary structure of every subunit.The resaults are far away from the expected.Not only proteins dont come closer but also they do strange movements destroying their structure.There is no sign of hydrophobic effect too.Is there a possible explanation?(I have diilectric=20,temperature=300 k,exclude 1-2)Should i change the parameters of the simulation or such a force field would never give an expected protein-protein interaction??thank u in advance!
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