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

James Starlight jmsstarlight at gmail.com
Thu Jan 17 07:24:22 CET 2013

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)
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 ?


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