A problem in ABF simulation

From: 宋瑞珩 (141130085_at_smail.nju.edu.cn)
Date: Tue Nov 29 2016 - 04:28:21 CST

Dear all

I used the RMSD as a reaction coordinate to calculate the potential surface of a conformation change. I set the RMSD boundary ranging from 3.4 to 3.6 and the lower wall constant to be 100, as the tutorial said. However, I found the RMSD value in the output file went beyond my constraints and decreased to 3.1. I tried to increase the wall constant to 100000, but it still did not work. Does anyone know how to solve this problem? Here is my input file:




Colvarstrajfrequency 100

Colvarsrestartfrequency 1000




colvar {

        name RMSD

        width 0.01

        lowerboundary 3.4

        upperboundary 3.6

        lowerwallconstant 100.0

        upperwallconstant 100.0

        rmsd {

                atoms {

                atomsFile 3.5.pdb

                atomsCol B

                atomsColvalue 1.00

                }

                refPositionsFile ref.pdb

                refPositionsCol B
 
                refPositionsColValue 1.00

         }

}




abf {

        colvars RMSD

        fullSamples 500

        hideJacobian

}

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