[gmx-users] lincs warning during simulatiion of open-to-close transitions

[James Starlight]

Dear Gromacs Users!


I'm simulatting open to close transition of calmodulin by means of
essential dynamics sampling. When my protein reaches closed state
(this time both ef hands domains aproach each other) I've obtain set
of lincs warnings and my simulatting crashes. I'm using gpu-based
gromacs with the sd integrator (As the thermostat). Below you can see
parameters for lincs options

constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy


Does it possible to resolve such problem by means of modification of
lincs options in mdp file ?



James