[gmx-users] Brownian Dynamics - Tabulated Potential
gmx3 at hotmail.com
Thu Mar 11 17:04:32 CET 2010
If you read the manual carefully, you would have noticed that the potential
is interpolated using cubic spline interpolation and the forces are the derivative
of these splines. Your scheme would work if the forces would be interpolated linearly.
> From: junsookim76 at gmail.com
> To: gmx-users at gromacs.org
> Date: Thu, 11 Mar 2010 10:55:03 -0500
> Subject: [gmx-users] Brownian Dynamics - Tabulated Potential
> I am trying the brownian dynamics simulations of a polymer chain using
> FENE potential and some effective potential. For this purpose, I made
> tabulated potentials for polymer bonds and non-bonded interactions,
> and the simulations are running fine.
> As far as I know, the Brownian dynamics simulations only need the
> forces at each time step (eq. 3.64 in Manual). So I tested the BD
> simulation by setting the potential energy equal to Zero while keeping
> the force unchanged. Then I have a problem with simulations. The bonds
> are broken. I do not understand why we need the potential energy in
> Brownian dynamics simulations. It would be really appreciated if
> anyone provides any hint.
> Here is a piece of the bonding tabulated potential of FENE with the
> potential set as zero and the force unchanged.
> Jun Soo
> # r U(r) -U'(r)
> 4.950 0.00000 11.5494
> 4.952 0.00000 9.29470
> 4.954 0.00000 7.10307
> 4.956 0.00000 4.97242
> 4.958 0.00000 2.90067
> 4.960 0.00000 0.885859
> 4.962 0.00000 -1.07395
> 4.964 0.00000 -2.98060
> 4.966 0.00000 -4.83590
> 4.968 0.00000 -6.64158
> 4.970 0.00000 -8.39931
> 4.972 0.00000 -10.1107
> 4.974 0.00000 -11.7774
> 4.976 0.00000 -13.4008
> 4.978 0.00000 -14.9825
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