Hello,
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.
Quoting:
"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?
Thanks,
Chris.
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