[gmx-users] Problem running free energy simulations

Michael Shirts mrshirts at gmail.com
Thu Oct 3 05:54:28 CEST 2013

Sounds like the simulation is blowing up.  How soon does it start crashing.

Also, what configurations are you using to start your free energy
simulations at each lambda?

On Wed, Oct 2, 2013 at 10:31 PM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> 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.
> Thanks,
> Jernej
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