[gmx-users] Problem running free energy simulations

Jernej Zidar jernej.zidar at gmail.com
Thu Oct 3 04:31:08 CEST 2013

Hi all,
  I'm trying to determine the free energy of solvation for a molecule
in n-octanol. I'm separately turning off the Coulomb and Lennard-Jones
interactions as instructed in the free energy tutorial. The
Lennard-Jones simulations keep on crashing for most values of lambda
with the message:
Program mdrun, VERSION 4.6.3
Source code file: /home/zidar/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
1 of the 79007 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1 nm) or the two-body cut-off distance (1 nm), see option
-rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

- - -

  I tried using "-noddcheck", "-pd" (separate simulations) but the
simulations still fail.

  The molecule surveyed is not charged (branched hydrocarbon) and I
can simulate it using any ensemble without a problem. I'm using CgenFF
without adding any new atom types so all the interactions should be
properly accounted for.

  Any advice on how to solve this will be greatly appreciated. I was
able to perform free energy simulations of a similar molecule in
octanol without any major problem.


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