[gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

Eric Smoll ericsmoll at gmail.com
Fri Apr 14 01:42:47 CEST 2017

Hello GROMACS users,

I am running NVT alchemical free energy simulations (change in atom number,
bonding, etc.). These simulations appear to go well at all lambda values
below 1.0 (no errors and the resulting trajectories show no unusual
behaviour). At lambda=1.0, the system returns an error before or during the
first step:


*WARNING: Listed nonbonded interaction between particles 376 and 384 at
distance 4.655 which is larger than the table limit 2.500 nm. This is
likely either a 1,4 interaction, or a listed interaction insidea 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 willonly see this
message once, even if it occurs for several interactions.IMPORTANT: This
should not happen in a stable simulation, so there isprobably something
wrong with your system. Only change the table-extensiondistance in the mdp
file if you are really sure that is the reason.*"

However the same system (input structure + topology + mdp-settings) will
minimize without any issue at same lambda=1.0 setting. If I increase the
table-extension distance to 4.0 nm, the distance reported in the error gets
very large:

*WARNING: Listed nonbonded interaction between particles 541 and 554 at
distance 183739120.000 which is larger than the table limit 5.500 nm.*"

I am not sure what is going wrong.


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