[gmx-users] Brownian Dynamics - Tabulated Potential

[Jun Soo Kim]

Hi,

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.

Thanks,
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