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
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
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.
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