Strange-looking RDFs for glycine and water simulation

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1

Hello,

I've simulated a mixture of 500 glycine molecules in a ~6.3 nm box, dissolved in water. I looked at the plots for energy and temperature and nothing seems abnormal about them: http://imgur.com/fIdCK0f. However, my radial distribution functions look very wrong: http://imgur.com/J6wN77G. I'm wondering if there is a problem with my input script or if you think I need to double check the parameters for all of my atoms, or if something else might be causing problems. Here's my input script: https://justpaste.it/kei6. I left in my comments - I hope they aren't distracting. I also looked at the movie in vmd, but saw no obvious problems. No atoms were flying around and it didn't look too compressed. I struggled and failed to make a .gif of it though so I can't show that - sorry.

Thanks very much for any help,
Nathan

2

If you are not matching peaks at small r, note this from the

compute rdf doc page:

IMPORTANT NOTE: If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the RDF. One way to get around this, is to write a dump file, and use the rerun command to compute the RDF for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.

Steve