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

James Starlight jmsstarlight at gmail.com
Thu Jan 17 19:24:36 CET 2013

In addition to LINCS warning during last simulation I obtained the
next warning from mdrun (again that was when calmodulin reached close
compact conformation)

WARNING: Listed nonbonded interaction between particles 1230 and 1249
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

what does it mean and how I could avoid it ?

2013/1/17 James Starlight <jmsstarlight at gmail.com>:
> 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

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