[gmx-users] free energy and soft core

Frauke Meyer fmeyer at iris3.simm.ac.cn
Fri Aug 6 04:57:52 CEST 2004

Hi all,

for the perturbation of a ligand (A) to dummy atoms (B) I want to use
soft core potential. With

free_energy              = yes
init_lambda              = 0
delta_lambda             = 0.000001
sc-alpha                 = 1.5
sc-sigma                 = 0.3

I get LINCS warnings after the first few steps and mdrun crashes,

sc-alpha                 = 0
sc-sigma                 = 0.3

the whole perturbation runs fine (though with the expected singularities
for lambda near to 1).

Surprisingly, with larger sc-alpha (eg. 10) LINCS warnings are fewer and
stop after some steps, and the perturbation terminates normally.
What might the problem here be? Topology B (dummies covalently boudn to
each other) anyway has no dispersion. I expected less warnings and
results to alpha=0 with *lowering* alpha, but did not find that.

Another surprise was that the dynamics depend on sc-sigma: Higher
has the same effects a higher sc-alpha. But should not sigma_A be
calculated brom C6_A and C12_A, and sigma_B not play a role, because
C6_B = C12_B = 0 anyway, so that sc-alpha is not used for the distortion
of LJ?

Or what is my misunderstanding here?

Thanks for any advice,

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