We would like to use the sander API to do some energy evaluation of some
simple systems. Part of the goal is to avoid lots of unnecessary disk I/O.
Therefore, we would like to create topology and coordinate information
within our own program and keep it resident in memory. The coordinates are
easy enough, but I don't see anything in the manual about what data
structure holds the topology information and how we can access it. All of
the examples simply use the sander_setup_mm() function to read a topology
file from disk.
Maybe there are too many idiosyncrasies in the topology construction and we
should just go ahead and use leap or parmed to do that. But our situation
is very simple, We are modeling a crystal lattice, so there are no bonds
just some ions with VDW parameters and charges. I feel like this is simple
enough that we ought to be able to create this ourselves and pass it to the
sander API.
Any information or examples would be appreciated. Oh, and we are using C,
but I suppose we could use anything else if that would make life easier.
Thanks,
Brent
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Tue May 16 2017 - 07:00:02 PDT
