On Mon, Dec 01, 2014, Jorgen Simonsen wrote:
>
> Thanks for helping me out here because I am quite lost in how to fix the
> problem for the moment. There is clearly something going wrong with the
> extra points but I am not quite sure why this is added or when it is added.
Thanks for sending the files. Having an actual example is *so* much more
helpful than just a description in an email.
1. Please ignore my earlier comments. The extra points routine is
re-computing 1-4 nonbonded terms (even when you don't have any extra points).
For some reason, the code to re-compute 1-4 terms is failing with so many
bonds to a single central atom. It's not clear why this is happening--
I'll enter a bug in our tracking system.
2. A workaround is to set ntb=0, igb=6. I'm not sure if this will work for
your "real" system, i.e. if you need to set up a PBC simluation with explicit
solvent, for example. If you get to that step and see the same problem, be
sure to try pmemd as well as sander...they might have different algorithms
here.
...good luck...dac
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Received on Tue Dec 02 2014 - 05:30:02 PST
