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

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 19:28:47 CET 2013

On 1/17/13 1:24 PM, James Starlight wrote:
> 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 ?

Note the "IMPORTANT" statement.  Your system is blowing up.  Whatever you're 
doing is causing the physical model to fail.


> 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


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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