This looks like one manifestation of "the model physics is broken, and so
is the resulting simulation system." Does your implementation behave for
standard parameter values?
On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. <chapma...@ornl.gov>
> Hello all,
> I am trying to model TIP4P/2005f water using Gromacs 5.1.2. Specifically,
> I'm trying to show how modifying the parameters of the TIP4P/2005f model
> changes the density of states. I wrote a small script to randomly vary the
> parameters and write out the .gro and .top files. When I tried running my
> molecular dynamics run, however, I got the following message:
> A list of missing interactions:
> Morse of 686 missing 1
> Molecule type 'WAT'
> the first 10 missing interactions, except for exclusions:
> Morse atoms 1 3 global 69 71
> Fatal error:
> 1 of the 1029 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (0.294303 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
> I'm trying to figure out if this error is because the random values for
> the parameters I chose were bad values (I sample them from a log-normal
> distribution with a mean of the defined values of the TIP4P/2005f values
> and a variance of 1% of those values), or if my script is writing out the
> .gro and .top files incorrectly, or some other cause. Any help that could
> be provided would be greatly appreciated.
> Thank you,
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