Hi,
On Wed, Aug 21, 2013 at 11:34 AM, Jose Borreguero <borreguero.gmail.com> wrote:
> I looked at BONDS_WITHOUT_HYDROGEN and the indexes pointing to the
> BOND_FORCE_CONSTANT entries are different in the two prmtop files, indeed
> indicating the different ordering of the force constants. Thus, the
> topologies seem to be the same in both files :) I also opened xparmed.py
> and printed a few bonds, and they came out the same.
As one final test, you could run some short MD or minimization (single
thread) with each topology using the same initial coordinates, random
seed (ig), etc for both - all energy terms should match.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Aug 21 2013 - 12:30:03 PDT
