AMBER Archive (2005)

Subject: Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Tue Apr 26 2005 - 03:37:01 CDT

Dear Ilyas, Amber List

I have attempted the same modification of the sander mixing rule that you
tried, to enable the starting state to have dummy atoms.

We probably did very similar code modifications, and I ran into a problem
that sounds a little like yours.

That is, my modifikation works fine for a nonperiodic system (giving
exactly symmetrical dvdl curves, only different in the sign) but they give
strange results when I activate periodic boundary conditions.

I think this is not a TI problem but something in the way sander handles
dummy atom in the starting state. Unfortunately I could not pinpoint the
error any better than this, due to lack of programming skills...

Kind Regards,

Thomas

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