adding constraints

From: doty alexiou (
Date: Thu Nov 26 2009 - 15:40:09 CST

I am trying to make a CG simulation of a protein in order to study protein-protein interaction. I read at : Four-scale description of membrane sculpting by Ba-domains(Anton Arkhipov,Ying Yin, Klaus Schulten), that i have to add harmonic contsraints to preserve the tertiary structure. I guess that I have to add the harmonic constraints parameters in the configuration file. But how should look like a consref file and a conskfile? Can i find an example of this kind of files?

Shall i also specify a certain direction (X,Y,Z)?

In order to chose the right constant i guess i should monitore the dynamics of the protein..but how exactly?I dont have a membrane,so should i let the CGprotein alone ''running'' using different constants and then chose which is closer to the all-atom ''running''?

Thank you in advance!

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