A problem in ABF simulation

From: 宋瑞珩 (141130085_at_smail.nju.edu.cn)
Date: Wed Dec 14 2016 - 05:45:28 CST

Dear all

I used the RMSD as a reaction coordinate to calculate the potential surface of a conformation change. I found the free energy decreased steeply with the reaction coordinate(the gradient is about -100kcal/A, this is quite a large value). However, the previous MD simulation in NPT ensemble revealed that the initial state(rmsd=1) had a lower energy than the final state(rmsd=4), and the energy difference between the two states was about 100kcal/mol. I have no idea about the paradox. Can anyone give some suggestions? Here is my input file:

Colvarstrajfrequency 100

Colvarsrestartfrequency 1000

colvar {

        name RMSD

        width 0.01

        lowerboundary 1.0

        upperboundary 4.0

        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


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