[gmx-users] pull code, lambda, and soft core availability

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Feb 12 20:33:42 CET 2009


I see from looking at the source code that the free-energy lambda  
dependence is now available to the pull code based on pull_kB1.  
However, this leads to serious problems converging near lambda=1 when  
pull_k1=large and pull_kB1=0 and in the absence of a restraint (with  
k=0) the pulled COM is allowed to sample a large volume. I suspect  
that a soft core lambda dependence would help here, but the  
descriptions in the .mpd options section of the online manual indicate  
that this is available only for Lj and coulombic.

"sc_alpha: (0) the soft-core parameter, a value of 0 results in linear  
interpolation of the LJ and Coulomb interactions"

Does anybody know if it is possible to get soft core potentials for an  
arbitrary coordinate?

I tested the application of this myself by bypassing the free energy  
code and simply modifying the A-state pull_k1 value based on lambda  
0->1 and then calculating dGdl from the px.xvg file myself. However, I  
am unclear how one would implement this as soft core. Does anybody  
know of a good paper that describes the underlying equations that  
define soft core?


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