I am currently simulating a molecule in explicit water with OpenMM with
prmtop and inpcrd created by AMBER form a pdb. I'm having a problem
simulating the molecule for a long time because the molecule of interest
eventually reaches the edge of the box of water and is partially out, which
I would assume would affect the simulation.
I would like to know if there was a command somewhere where I can make
certain atoms static so they do not move positions at all, which would
solve this problem.
These are the commands I do to make the prmtop and inpcrd:
http://pastebin.com/raw.php?i=1xSj1eF2
Thanks!!
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Received on Tue Feb 05 2013 - 23:30:02 PST
