From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Dec 14 2016 - 10:29:51 CST
Hi,
The Jacobian term in that PMF is approximately (RT*(3N-4) / x), so the
difference of 100 kcal/mol you see is entirely expected if about 50 atoms
are involved in the definition of the coordinate.
Jerome
On 14 December 2016 at 12:45, 宋瑞珩 <141130085_at_smail.nju.edu.cn> wrote:
> 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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